16PK
PHOSPHOGLYCERATE KINASE FROM TRYPANOSOMA BRUCEI BISUBSTRATE ANALOG
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 13PK | PDB ENTRY 13PK |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 7.7 | VAPOR DIFFUSION BY MIXING, pH 7.7, vapor diffusion |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.64 | 53 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 72.71 | α = 90 |
b = 79.76 | β = 90 |
c = 81.32 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | IMAGE PLATE | MARRESEARCH | 1997-05-21 | M |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL9-1 | SSRL | BL9-1 |
Data Collection
Overall | |||||||||||||||||||
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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 | 1.58 | 21 | 99.7 | 0.052 | 60549 | 2 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work (Depositor) | R-Free (Depositor) | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 13PK | 1.6 | 8 | 2 | 65142 | 4593 | 97.3 | 0.188 | 0.188 | 0.235 | RANDOM | 16.5 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
x_scangle_it | 2.5 |
x_mcangle_it | 2 |
x_scbond_it | 2 |
x_mcbond_it | 1.5 |
x_angle_deg | 1.41 |
x_bond_d | 0.008 |
x_bond_d_na | |
x_bond_d_prot | |
x_angle_d | |
x_angle_d_na |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 3206 |
Nucleic Acid Atoms | |
Solvent Atoms | 580 |
Heterogen Atoms | 54 |
Software
Software | |
---|---|
Software Name | Purpose |
X-PLOR | model building |
X-PLOR | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |
X-PLOR | phasing |