4FIO
Crystal Structure of Methenyltetrahydromethanopterin Cyclohydrolase from Methanobrevibacter ruminantium
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1QLM | PDB ENTRY 1QLM |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 8.5 | 293 | 0.2 M sodium acetate, 0.1 M Tris-HCl, 30% (w/v) PEG 4000 and 3% (v/v) isopropanol, pH 8.5, VAPOR DIFFUSION, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.13 | 42.12 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 52.37 | α = 120.06 |
b = 74.855 | β = 100.01 |
c = 74.816 | γ = 98.28 |
Symmetry | |
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Space Group | P 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 | 100 | CCD | ADSC QUANTUM 315r | 2011-04-28 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | AUSTRALIAN SYNCHROTRON BEAMLINE MX2 | Australian Synchrotron | MX2 |
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 | 1.37 | 19.88 | 93.8 | 17.3 | 3.7 | 184543 | 1 |
Highest Resolution Shell | |||||||||||||||||||
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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) | ||||||||||
1 | 1.37 | 1.44 | 79.6 | 0.606 | 0.606 | 2.2 |
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 | PDB ENTRY 1QLM | 1.37 | 19.88 | 175155 | 9299 | 93.7 | 0.132 | 0.13 | 0.175 | RANDOM | 18.55 |
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] | |
2.07 | 0.72 | -1.55 | -0.44 | 4.45 | -1.63 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.407 |
r_sphericity_free | 19.25 |
r_dihedral_angle_4_deg | 16.144 |
r_dihedral_angle_3_deg | 13.995 |
r_sphericity_bonded | 10.757 |
r_rigid_bond_restr | 8.441 |
r_dihedral_angle_1_deg | 5.94 |
r_angle_refined_deg | 2.297 |
r_chiral_restr | 0.164 |
r_bond_refined_d | 0.023 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7144 |
Nucleic Acid Atoms | |
Solvent Atoms | 1071 |
Heterogen Atoms | 24 |
Software
Software | |
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Software Name | Purpose |
Blu-Ice | data collection |
MOLREP | phasing |
REFMAC | refinement |
XDS | data reduction |
SCALA | data scaling |