2YXB

Crystal structure of the methylmalonyl-CoA mutase alpha-subunit from Aeropyrum pernix


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1oil batch2930.4M Ammonium dihydrogen phosphate, oil batch, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
1.66220726.00201

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.902α = 90
b = 51.134β = 90
c = 54.564γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU JUPITER 210mirrors2006-10-15MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL26B20.97884, 0.90000, 0.97938SPring-8BL26B2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.85099.80.06717.86.611582-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.8698.90.352.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMADTHROUGHOUT1.837.271097055299.560.213730.211940.24713RANDOM33.745
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]
-0.790.520.27
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it6.835
r_dihedral_angle_1_deg6.365
r_scbond_it4.419
r_mcangle_it2.888
r_angle_refined_deg2.166
r_mcbond_it1.633
r_angle_other_deg1.002
r_nbd_other0.255
r_symmetry_vdw_refined0.252
r_nbd_refined0.222
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it6.835
r_dihedral_angle_1_deg6.365
r_scbond_it4.419
r_mcangle_it2.888
r_angle_refined_deg2.166
r_mcbond_it1.633
r_angle_other_deg1.002
r_nbd_other0.255
r_symmetry_vdw_refined0.252
r_nbd_refined0.222
r_symmetry_vdw_other0.219
r_symmetry_hbond_refined0.204
r_xyhbond_nbd_refined0.2
r_chiral_restr0.148
r_nbtor_other0.092
r_bond_refined_d0.033
r_gen_planes_refined0.009
r_gen_planes_other0.004
r_bond_other_d0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1074
Nucleic Acid Atoms
Solvent Atoms79
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing