4LZT
ATOMIC RESOLUTION REFINEMENT OF TRICLINIC HEW LYSOZYME AT 295K
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2LZT | PDB ENTRY 2LZT |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | batch method | 4.5 | BATCH METHOD USED. 1% PROTEIN SOLUTION IN 100MM SODIUM ACETATE PH 4.5-4.6. SODIUM NITRATE ADDED TO A CONCENTRATION OF 20MGS/ML. CRYSTALS GROWN AT ROOM TEMPERATURE., batch method |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.82 | 31.8 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 27.24 | α = 88.52 |
b = 31.87 | β = 108.53 |
c = 34.23 | γ = 111.89 |
Symmetry | |
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Space Group | P 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 295 | IMAGE PLATE | MARRESEARCH | BENT MIRROR | 1996-12-09 | M |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | EMBL/DESY, HAMBURG BEAMLINE BW7B | EMBL/DESY, HAMBURG | BW7B |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym I (Observed) | Net I Over Average Sigma (I) | Redundancy | Number Reflections (All) | Number Reflections (Observed) | Observed Criterion Sigma (F) | Observed Criterion Sigma (I) | B (Isotropic) From Wilson Plot | |||||||
1 | 0.95 | 21 | 96.5 | 0.06 | 0.06 | 14.4 | 2 | 61265 | -3 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
0.95 | 0.97 | 94.9 | 0.273 | 0.273 | 4.7 | 2 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | STRUCTURE KNOWN | FREE R | PDB ENTRY 2LZT | 0.95 | 21 | 61258 | 1870 | 96.5 | 0.1082 | 0.1144 | 0.147 | RANDOM |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
Coordinate Error | ||
---|---|---|
Structure Solution Method | Refinement High Resolution | Refinement Low Resolution |
15 | 920.89 | 1123.7 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
s_from_restr_planes | 0.39 |
s_non_zero_chiral_vol | 0.152 |
s_zero_chiral_vol | 0.128 |
s_approx_iso_adps | 0.095 |
s_similar_adp_cmpnt | 0.071 |
s_anti_bump_dis_restr | 0.044 |
s_angle_d | 0.033 |
s_bond_d | 0.016 |
s_similar_dist | 0.014 |
s_rigid_bond_adp_cmpnt | 0.007 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1020 |
Nucleic Acid Atoms | |
Solvent Atoms | 139 |
Heterogen Atoms | 24 |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
SHELXL-96 | model building |
SHELXL-96 | refinement |
SHELXL-96 | phasing |