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Streptomyces coelicolor methylmalonyl-CoA epimerase (S115T) 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 7 298 100 mM Bis-Tris:HCl pH 7.0, 700 mM ammonium sulfate, and 5% PEG400
Crystal Properties Matthews coefficient Solvent content 3.79 67.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.309 α = 90 b = 69.309 β = 90 c = 103.562 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 IMAGE PLATE MAR scanner 300 mm plate MD2 microdifractometer 2019-04-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
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) CC (Half) 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 1.5 30 99.9 0.112 0.101 0.116 0.031 0.994 492.4 13.9 41252 27.733
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.55 99.9 1.092 0.967 1.134 0.301 0.84 7 13.8
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 1.5 26.61 39173 2012 99.78 0.1544 0.1531 0.1529 0.1791 0.1792 RANDOM 27.733
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] 0.03 0.03 -0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.923 r_dihedral_angle_4_deg 12.977 r_dihedral_angle_3_deg 12.855 r_dihedral_angle_1_deg 7.495 r_angle_refined_deg 2.375 r_angle_other_deg 1.911 r_chiral_restr 0.273 r_bond_refined_d 0.017 r_gen_planes_refined 0.012 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.923 r_dihedral_angle_4_deg 12.977 r_dihedral_angle_3_deg 12.855 r_dihedral_angle_1_deg 7.495 r_angle_refined_deg 2.375 r_angle_other_deg 1.911 r_chiral_restr 0.273 r_bond_refined_d 0.017 r_gen_planes_refined 0.012 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1110 Nucleic Acid Atoms Solvent Atoms 275 Heterogen Atoms 67
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling PHASER phasing PDB_EXTRACT data extraction ARP/wARP model building HKL-2000 data reduction