1REQ
METHYLMALONYL-COA MUTASE
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | THE CRYSTALS WERE GROWN IN THE PRESENCE OF 2MM EXCESS 5'-DEOXYADENOSYLCOBALAMIN (COENZYME B12) AND 12MM DESULPHO-COA (FINAL CONCENTRATIONS), EQUILIBRATED AGAINST 14% W/V PEG 4000 AND 20% V/V GLYCEROL, 100MM TRIS PH 7.5. THE ELECTRON DENSITY MAPS SHOW NO ADENOSYL GROUP ATTACHED TO THE COBALT ATOM, AND SPECTRA FROM SIMILAR CRYSTALS SHOW EVIDENCE OF SUBSTANTIAL REDUCTION OF COIII TO COII, WHICH IS 5-COORDINATE. THE COBALAMIN IN THIS CRYSTAL STRUCTURE IS BEST CONSIDERED AS REDUCED COB(II)ALAMIN (OR B12R). THE BOND LENGTH FROM THE COBALT TO THE LOWER AXIAL LIGAND, NE2 OF HIS A 610 (OR HIS C 610) IS SIGNIFICANTLY LONGER THAN THAT IN MODEL COMPOUNDS. POORLY ORDERED LOOPS: DENSITY IN THE FOLLOWING REGIONS IS POOR, AND THE MODEL MUST BE CONSIDERED UNRELIABLE. ALPHA CHAIN: A 1, C 1 MISSING, A 2 - A 3, C 2 - C 3 WEAK. BETA CHAIN: B 1 - C 19, C 1 - C 16 MISSING; B 184 - B 191, D 184 - D 191 WEAK; D 228 - D 230 WEAK; D 271 - D 276 VERY POOR DENSITY (MUCH BETTER IN CHAIN B); D 315 WEAK; D 474 - D 428 WEAK. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.76 | 48 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 119.8 | α = 90 |
b = 161.3 | β = 105.1 |
c = 88.4 | γ = 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 | IMAGE PLATE | MAR scanner 300 mm plate | 1994-06-24 | M |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID2 | ESRF | ID2 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | 20 | 99.8 | 0.051 | 4.6 | 217377 | 5 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Work | R-Free | Mean Isotropic B | ||||||||||
X-RAY DIFFRACTION | 2 | 20 | 206327 | 10907 | 99.8 | 0.22 | 0.275 | 42 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
p_scangle_it | 5.8 |
p_scbond_it | 4.6 |
p_mcangle_it | 4.1 |
p_mcbond_it | 3.2 |
p_multtor_nbd | 0.256 |
p_xyhbond_nbd | 0.187 |
p_singtor_nbd | 0.183 |
p_chiral_restr | 0.156 |
p_planar_d | 0.044 |
p_angle_d | 0.039 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 20510 |
Nucleic Acid Atoms | |
Solvent Atoms | 1532 |
Heterogen Atoms | 330 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
MOSFLM | data reduction |