3REQ

METHYLMALONYL-COA MUTASE, SUBSTRATE-FREE STATE (POOR QUALITY STRUCTURE)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2REQPDB ENTRY 2REQ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION7.5PROTEIN SOLUTION: 20 MG/ML PROTEIN, 1MM ADENOSYLCOBALAMIN, 1MM DTT, TRIS PH 7.5. RESERVOIR: 14% PEG 4000 (W/V), 20% GLYCEROL (V/V), 100MM TRIS-HCL PH 7.5. EQUAL VOLUMES OF PROTEIN SOLUTION AND RESERVOIR MIXED, AND EQUILIBRATED BY VAPOR DIFFUSION., vapor diffusion
Crystal Properties
Matthews coefficientSolvent content
2.653

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 110.91α = 90
b = 110.91β = 90
c = 257.74γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 300 mm plate2 MIRRORS, 2 SI(111) CRYSTAL MONOCHROMATOR1996-06-09M
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM14ESRFBM14

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
12.72999.20.0727.9944606678
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)
12.72.8598.70.38126.8

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 2REQ2.72041745222497.60.3130.393RANDOM68
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_tor35
p_staggered_tor25
p_special_tor15
p_scangle_it6.1
p_planar_tor5.3
p_mcangle_it4.2
p_scbond_it4.2
p_mcbond_it2.6
p_multtor_nbd0.166
p_chiral_restr0.156
RMS Deviations
KeyRefinement Restraint Deviation
p_transverse_tor35
p_staggered_tor25
p_special_tor15
p_scangle_it6.1
p_planar_tor5.3
p_mcangle_it4.2
p_scbond_it4.2
p_mcbond_it2.6
p_multtor_nbd0.166
p_chiral_restr0.156
p_xyhbond_nbd0.133
p_singtor_nbd0.128
p_planar_d0.049
p_angle_d0.046
p_plane_restr0.03
p_bond_d0.012
p_angle_deg
p_hb_or_metal_coord
p_xhyhbond_nbd
p_orthonormal_tor
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10176
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms109

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
REFMACrefinement
CCP4data scaling