3PZ2
Crystal structure of RabGGTase(DELTA LRR; DELTA IG) in Complex with BMS3 and lipid substrate GGPP
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3DSS |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.2 | 284 | 14% (w/v) PEG3350, 0.2 M Ca(OAc)2, 0.1 M HEPES, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 284K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.2 | 44.15 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 66.448 | ¦Á = 90 |
b = 84.582 | ¦Â = 90 |
c = 117.973 | ¦Ã = 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 | MARMOSAIC 225 mm CCD | 2008-10-12 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X10SA | 1.0000 | SLS | X10SA |
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 | 2.35 | 30 | 99.4 | 0.063 | 17.5 | 4.9 | 28375 | 28201 | 5 | 42.4 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.35 | 2.45 | 99 | 0.377 | 7.1 | 5 | 3230 |
Refinement
Statistics | |||||||||||||||||||
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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 | 3DSS | 2.35 | 30 | 26810 | 1403 | 99.5 | 0.19095 | 0.18761 | 0.25551 | RANDOM | 37.329 |
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] | |
-1.18 | 1.47 | -0.3 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.004 |
r_dihedral_angle_3_deg | 19.375 |
r_dihedral_angle_4_deg | 18.32 |
r_dihedral_angle_1_deg | 7.416 |
r_scangle_it | 5.164 |
r_angle_other_deg | 4.262 |
r_mcbond_other | 4.144 |
r_scbond_it | 3.523 |
r_mcangle_it | 2.638 |
r_angle_refined_deg | 1.622 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4920 |
Nucleic Acid Atoms | |
Solvent Atoms | 183 |
Heterogen Atoms | 69 |
Software
Software | |
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Software Name | Purpose |
PHASER | phasing |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |