4GVR
X-ray structure of the Archaeoglobus fulgidus methenyl-tetrahydromethanopterin cyclohydrolase
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.6 | 291 | 10% (w/v) PEG 4000, 10% (v/v) Isopropanol, 0.1M Sodium acetate pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.71 | 54.63 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 118.54 | α = 90 |
b = 122.08 | β = 99.02 |
c = 79.39 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 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 | 2011-12-08 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X10SA | 1.0001 | SLS | X10SA |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 1.52 | 48.17 | 170753 | 164493 |
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 | 1QLM | 1.52 | 48.17 | 156241 | 8252 | 96.33 | 0.16754 | 0.16425 | 0.23124 | RANDOM | 25.003 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
0.39 | 0.17 | -0.16 | -0.17 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_sphericity_free | 39.415 |
r_dihedral_angle_2_deg | 35.563 |
r_sphericity_bonded | 22.006 |
r_dihedral_angle_4_deg | 20.294 |
r_dihedral_angle_3_deg | 14.329 |
r_dihedral_angle_1_deg | 6.863 |
r_rigid_bond_restr | 5.309 |
r_angle_refined_deg | 1.89 |
r_chiral_restr | 0.145 |
r_bond_refined_d | 0.018 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7308 |
Nucleic Acid Atoms | |
Solvent Atoms | 740 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data collection |
PHASER | phasing |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |