2REQ

METHYLMALONYL-COA MUTASE, NON-PRODUCTIVE COA COMPLEX, IN OPEN CONFORMATION REPRESENTING SUBSTRATE-FREE STATE


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1REQPDB ENTRY 1REQ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION7.5PROTEIN SOLUTION: 20 MG/ML PROTEIN, 1MM ADENOSYLCOBALAMIN, 2MM COA, 1MM DTT, TRIS -HCL PH 7.5. RESERVOIR SOLUTION: 17.5% (W/V) PEG4000, 20% GLYCEROL (V/V), 100MM TRIS-HCL PH 7.5. EQUAL VOLUMES OF PROTEIN SOLUTION WERE MIXED AND EQUILIBRATED BY VAPOR DIFFUSION., vapor diffusion
Crystal Properties
Matthews coefficientSolvent content
2.856

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 104.95α = 90
b = 162.06β = 108.75
c = 104.2γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 180 mm plateTOROIDAL MIRROR, SI MONOCHROMATOR1995-07-01M
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONELETTRA BEAMLINE 5.2RELETTRA5.2R

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.52099.80.09264.81135123.555
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.52.6499.70.3382.13.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1REQ2.520113303453899.60.2590.325RANDOM47
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]
RMS Deviations
KeyRefinement Restraint Deviation
p_transverse_tor34.4
p_staggered_tor19.8
p_planar_tor5.9
p_scangle_it5.102
p_mcangle_it3.74
p_scbond_it3.713
p_mcbond_it2.424
p_multtor_nbd0.17
p_chiral_restr0.141
p_singtor_nbd0.129
RMS Deviations
KeyRefinement Restraint Deviation
p_transverse_tor34.4
p_staggered_tor19.8
p_planar_tor5.9
p_scangle_it5.102
p_mcangle_it3.74
p_scbond_it3.713
p_mcbond_it2.424
p_multtor_nbd0.17
p_chiral_restr0.141
p_singtor_nbd0.129
p_xyhbond_nbd0.128
p_planar_d0.046
p_angle_d0.041
p_plane_restr0.03
p_bond_d0.012
p_angle_deg
p_hb_or_metal_coord
p_xhyhbond_nbd
p_orthonormal_tor
p_special_tor
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms20360
Nucleic Acid Atoms
Solvent Atoms636
Heterogen Atoms244

Software

Software
Software NamePurpose
AMoREphasing
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling