2ZUV
Crystal structure of Galacto-N-biose/Lacto-N-biose I phosphorylase in complex with GlcNAc, Ethylene glycol, and nitrate
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 6.5 | 277 | Na cacodyrate, Mg(NO3)2, PEG 4000, GlcNAc, pH 6.5, VAPOR DIFFUSION, temperature 277K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.23 | 44.83 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 204.043 | α = 90 |
b = 68.02 | β = 108.79 |
c = 116.047 | γ = 90 |
Symmetry | |
---|---|
Space Group | C 1 2 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 95 | CCD | ADSC QUANTUM 210 | 2007-06-04 | M | SINGLE WAVELENGTH | ||||||
2 | 1 | x-ray | 100 | CCD | ADSC QUANTUM 315 | 2006-11-29 | M | MAD |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PHOTON FACTORY BEAMLINE AR-NW12A | 1.000 | Photon Factory | AR-NW12A |
2 | SYNCHROTRON | PHOTON FACTORY BEAMLINE BL-5A | 0.97934, 0.97974, 0.96450 | Photon Factory | BL-5A |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | ||||||||
1,2 | 1.85 | 50 | 98.5 | 0.068 | 21.811 | 3.8 | 126352 | 19.7 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1.85 | 1.92 | 97.7 | 0.25 | 2.7 | 3.9 | 12453 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | 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 | Identical protein belonging to different space group | 1.85 | 35.14 | 126337 | 6359 | 98.37 | 0.151 | 0.149 | 0.192 | RANDOM | 22.142 |
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] | |
-0.01 | 0.01 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.016 |
r_dihedral_angle_4_deg | 18.325 |
r_dihedral_angle_3_deg | 12.587 |
r_dihedral_angle_1_deg | 5.821 |
r_scangle_it | 3.242 |
r_scbond_it | 2.044 |
r_angle_refined_deg | 1.325 |
r_mcangle_it | 1.287 |
r_mcbond_it | 0.724 |
r_chiral_restr | 0.098 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 11787 |
Nucleic Acid Atoms | |
Solvent Atoms | 1826 |
Heterogen Atoms | 94 |
Software
Software | |
---|---|
Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
MOLREP | phasing |