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Methylmalonyl-CoA epimerase in complex with 2-nitronate-propionyl-CoA
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, 2.6 M ammonium sulfate, 5% PEG 400
Crystal Properties Matthews coefficient Solvent content 1.86 34.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.837 α = 90 b = 68.837 β = 90 c = 103.37 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 2017-02-08 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 1.37 30 99.8 0.059 0.059 0.061 0.016 14.2 14.2 52867 -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 1.37 1.42 100 0.47 0.47 6.516 13.3
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1JC5 1.37 25.86 50250 2548 99.74 0.1486 0.1474 0.1736 0.2143 RANDOM 19.115
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] 0.19 0.19 -0.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.574 r_dihedral_angle_4_deg 13.827 r_dihedral_angle_3_deg 12.545 r_dihedral_angle_1_deg 7.452 r_angle_refined_deg 2.617 r_angle_other_deg 1.653 r_chiral_restr 0.287 r_bond_refined_d 0.021 r_gen_planes_refined 0.012 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.574 r_dihedral_angle_4_deg 13.827 r_dihedral_angle_3_deg 12.545 r_dihedral_angle_1_deg 7.452 r_angle_refined_deg 2.617 r_angle_other_deg 1.653 r_chiral_restr 0.287 r_bond_refined_d 0.021 r_gen_planes_refined 0.012 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1109 Nucleic Acid Atoms Solvent Atoms 314 Heterogen Atoms 74
Software Software Software Name Purpose HKL-2000 data reduction PHASER phasing SCALEPACK data scaling ARP/wARP model building Coot model building REFMAC refinement PDB_EXTRACT data extraction