3OKP
Crystal structure of Corynebacterium glutamicum PimB' bound to GDP-Man (orthorhombic crystal form)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3OKA | PDB entry 3oka |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 6.1 | 291 | 0.1 M DL-malic acid pH 6.1, 13% PEG 3350 , VAPOR DIFFUSION, temperature 291K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.51 | 51.08 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 44.746 | α = 90 |
b = 87.002 | β = 90 |
c = 106.895 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 QUANTUM 315r | 2010-02-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04 | 0.9763 | Diamond | I04 |
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 | 2 | 37.29 | 100 | 0.096 | 0.096 | 18.3 | 7.2 | 28997 | 28997 | 15.9 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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) | ||||||||||
2 | 2.11 | 99.8 | 0.38 | 0.38 | 5.7 | 7.2 | 4147 |
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 (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 3oka | 2 | 37.29 | 27519 | 27519 | 1476 | 99.93 | 0.20408 | 0.20256 | 0.2321 | RANDOM | 14.231 |
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] | |
-0.21 | 0.05 | 0.16 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.301 |
r_dihedral_angle_3_deg | 12.804 |
r_dihedral_angle_4_deg | 11.101 |
r_dihedral_angle_1_deg | 4.856 |
r_scangle_it | 1.076 |
r_angle_refined_deg | 1.022 |
r_scbond_it | 0.65 |
r_mcangle_it | 0.432 |
r_nbtor_refined | 0.292 |
r_mcbond_it | 0.259 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2827 |
Nucleic Acid Atoms | |
Solvent Atoms | 175 |
Heterogen Atoms | 28 |
Software
Software | |
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Software Name | Purpose |
ADSC | data collection |
PHASER | phasing |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |