4HAP
Crystal Structure of a GH7 family cellobiohydrolase from Limnoria quadripunctata in complex with cellobiose
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 4GWA |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 4.5 | 289 | 0.1M Sodium Acetate, 15% w/v PEG 6000, 0.5M CaCl2, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.18 | 43.48 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 52.26 | α = 94.26 |
b = 54.19 | β = 96.02 |
c = 72.45 | γ = 94.99 |
Symmetry | |
---|---|
Space Group | P 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | PIXEL | DECTRIS PILATUS 6M | 2012-05-06 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I02 | 0.9173 | Diamond | I02 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 1.6 | 71.795 | 93.4 | 0.113 | 7.6 | 3.3 | 96748 | 96748 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Rrim I (All) | Rpim I (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 1.6 | 1.69 | 91.9 | 0.595 | 0.595 | 0.721 | 0.4 | 1.2 | 3.1 | 13891 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 4GWA | 1.6 | 39.9 | 98248 | 96745 | 4846 | 93.43 | 0.1467 | 0.1444 | 0.1906 | RANDOM | 14.5747 |
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] | |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.348 |
r_dihedral_angle_4_deg | 23.012 |
r_dihedral_angle_3_deg | 13.388 |
r_dihedral_angle_1_deg | 6.63 |
r_angle_refined_deg | 2.009 |
r_angle_other_deg | 0.945 |
r_chiral_restr | 0.129 |
r_bond_refined_d | 0.021 |
r_gen_planes_refined | 0.011 |
r_bond_other_d | 0.002 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 6514 |
Nucleic Acid Atoms | |
Solvent Atoms | 1261 |
Heterogen Atoms | 59 |
Software
Software | |
---|---|
Software Name | Purpose |
MOSFLM | data reduction |
SCALA | data scaling |
PHASER | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
GDA | data collection |