3RMG
Crystal structure of geranylgeranyl pyrophosphate synthase from bacteroides thetaiotaomicron
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7 | 0.15M MALIC ACID, PH 7.0, 30% PEG 3350, 10% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.81 | 56.2 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 44.618 | ¦Á = 90 |
b = 111.408 | ¦Â = 92.56 |
c = 83.376 | ¦Ã = 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 | 93 | CCD | ADSC QUANTUM 315 | MIRRORS | 2010-06-03 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X29A | NSLS | X29A |
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 | 2.2 | 50 | 99.9 | 0.07 | 9.1 | 4.2 | 41607 | -5 | 46.037 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1 | 2.2 | 2.24 | 100 | 1.2 | 4.2 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | SAD | THROUGHOUT | 2.3 | 50 | 34960 | 1120 | 99.73 | 0.21522 | 0.21388 | 0.25819 | RANDOM | 66.598 |
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] | |
-1.5 | -2.2 | -0.78 | 2.08 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.879 |
r_dihedral_angle_4_deg | 19.87 |
r_dihedral_angle_3_deg | 17.05 |
r_scangle_it | 9.573 |
r_scbond_it | 6.255 |
r_mcangle_it | 4.945 |
r_dihedral_angle_1_deg | 4.443 |
r_mcbond_it | 3.218 |
r_angle_refined_deg | 0.915 |
r_chiral_restr | 0.058 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4547 |
Nucleic Acid Atoms | |
Solvent Atoms | 69 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
SHELX | model building |
RESOLVE | model building |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
SHELX | phasing |
RESOLVE | phasing |