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Crystal structure of human Methylmalonyl-CoA epimerase, MCEE
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3OA4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293.15 30% PEG smears (PEG400, PEG550 MME, PEG600, PEG1000), 0.1 M Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K
Crystal Properties Matthews coefficient Solvent content 2.37 48.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.12 α = 90 b = 66.69 β = 90.1 c = 76.98 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315 Kirkpatrick Baez bimorph mirror pair 2010-12-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 Diamond I02
Data Collection Overall 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 1.8 38.49 99.2 0.076 8.9 3.6 49557 49519 23
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.9 99.7 0.565 2 3.6 7219
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 30A4 1.8 36.59 2 49519 47027 2491 99.14 0.18961 0.18701 0.1913 0.23722 0.238 RANDOM 27.591
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] -2.33 0.11 2.72 -0.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.157 r_dihedral_angle_4_deg 20.022 r_dihedral_angle_3_deg 13.548 r_scangle_it 9.977 r_scbond_it 7.24 r_dihedral_angle_1_deg 7.083 r_mcangle_it 4.268 r_mcbond_it 2.883 r_angle_refined_deg 1.505 r_mcbond_other 0.932
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.157 r_dihedral_angle_4_deg 20.022 r_dihedral_angle_3_deg 13.548 r_scangle_it 9.977 r_scbond_it 7.24 r_dihedral_angle_1_deg 7.083 r_mcangle_it 4.268 r_mcbond_it 2.883 r_angle_refined_deg 1.505 r_mcbond_other 0.932 r_angle_other_deg 0.915 r_chiral_restr 0.093 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3983 Nucleic Acid Atoms Solvent Atoms 323 Heterogen Atoms 109
Software Software Software Name Purpose GDA data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling