7CC3
Versatile cis-prenyltransferase MM_0014 from Methanosarcina mazei (crystal type: co-FG)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 7CAQ |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 293 | 0.075 M succinic acid, pH7.0, 11% PEG 3350, and 25% glycerol |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.32 | 46.93 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 99.048 | ¦Á = 90 |
b = 99.221 | ¦Â = 90 |
c = 193.876 | ¦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 | PIXEL | DECTRIS PILATUS3 S 6M | 2018-06-26 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PHOTON FACTORY BEAMLINE BL-5A | 1.000 | Photon Factory | BL-5A |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | 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 | 1.72 | 48.5 | 100 | 0.052 | 1 | 42.6 | 22.3 | 202517 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.72 | 1.75 | 1.84 | 0.672 |
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 (All) | R-Work | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 7CAQ | 1.72 | 48.062 | 202517 | 9998 | 99.64 | 0.197 | 0.1963 | 0.2129 | 32.316 |
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] | |
0.01 | -0.024 | 0.013 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.758 |
r_dihedral_angle_4_deg | 18.884 |
r_dihedral_angle_3_deg | 13.63 |
r_dihedral_angle_1_deg | 6.184 |
r_lrange_it | 5.017 |
r_lrange_other | 4.988 |
r_scangle_it | 3.095 |
r_scangle_other | 3.095 |
r_mcangle_it | 2.569 |
r_mcangle_other | 2.569 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 13859 |
Nucleic Acid Atoms | |
Solvent Atoms | 781 |
Heterogen Atoms | 556 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
Aimless | data scaling |
MOLREP | phasing |