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Methylmalonyl-CoA epimerase in complex with methylmalonyl-CoA and NH4+
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JC5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 50 mM sodium chloride,
100 mM Bis-Tris:HCl pH 7.0,
2.3 M ammonium sulfate,
5% PEG 400
Crystal Properties Matthews coefficient Solvent content 3.69 66.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.537 α = 90 b = 68.537 β = 90 c = 103.15 γ = 90
Symmetry Space Group P 41 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 80 CCD RAYONIX MX300HE MD2 Micro Diffractometer 2017-07-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 1.55 30 100 0.087 0.087 0.09 0.024 11.4 14.4 36333 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.55 1.61 100 0.614 0.614 5.5 14.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 1JC5 1.55 29.4 34548 1719 99.7 0.1522 0.1513 0.1657 0.1699 0.1805 RANDOM 24.875
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] 0.47 0.47 -0.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.589 r_dihedral_angle_4_deg 14.052 r_dihedral_angle_3_deg 12.715 r_dihedral_angle_1_deg 7.331 r_angle_refined_deg 2.066 r_angle_other_deg 1.588 r_chiral_restr 0.113 r_bond_refined_d 0.016 r_gen_planes_refined 0.011 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.589 r_dihedral_angle_4_deg 14.052 r_dihedral_angle_3_deg 12.715 r_dihedral_angle_1_deg 7.331 r_angle_refined_deg 2.066 r_angle_other_deg 1.588 r_chiral_restr 0.113 r_bond_refined_d 0.016 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1109 Nucleic Acid Atoms Solvent Atoms 217 Heterogen Atoms 73
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PDB_EXTRACT data extraction ARP/wARP model building PHASER phasing HKL-2000 data reduction