2VGF
HUMAN ERYTHROCYTE PYRUVATE KINASE: T384M mutant
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2VGB | PDB ENTRY 2VGB |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 6.4 | pH 6.4 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.6 | 52.25 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 76.296 | α = 90 |
b = 172.976 | β = 93.12 |
c = 85.779 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 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 | 100 | CCD | ADSC CCD | 2000-06-10 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID14-2 | ESRF | ID14-2 |
Data Collection
Overall | |||||||||||||||||||
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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 | 2.75 | 20 | 93.7 | 0.08 | 5.6 | 2.2 | 52721 |
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 | 2.75 | 2.9 | 91.3 | 0.55 | 1.9 | 1.8 |
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 | PDB ENTRY 2VGB | 2.75 | 20 | 52721 | 1103 | 93.7 | 0.269 | 0.268 | 0.303 | RANDOM | 14.32 |
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] | |
-1.13 | -5.12 | 0.98 | -0.4 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.126 |
r_dihedral_angle_4_deg | 21.878 |
r_dihedral_angle_3_deg | 21.792 |
r_dihedral_angle_1_deg | 6.026 |
r_scangle_it | 3.114 |
r_angle_refined_deg | 1.79 |
r_scbond_it | 1.686 |
r_mcangle_it | 0.793 |
r_mcbond_it | 0.394 |
r_symmetry_vdw_refined | 0.365 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 15426 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms | 124 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
MOSFLM | data reduction |
CCP4 | data scaling |
CCP4 | phasing |