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Crystal structure of NADPH-dependent glyoxylate/hydroxypyruvate reductase SMc04462 (SmGhrB) from Sinorhizobium meliloti in apo form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5J23
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 3.5 289 0.2 ul of 14 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide, 0.5 mM TCEP and 5 mM NADPH were mixed with 0.2 ul of the MCSG Suite 3 condition #61 (0.1 M Citric acid pH=3.5, 2 M Ammonium sulfate) and equilibrated against 1.5 M NaCl solution in 96 Well 3 drop Crystallization Plate (Swissci). The protein was crystallized with the His-tag
Crystal Properties Matthews coefficient Solvent content 2.9 57.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 176.583 α = 90 b = 176.583 β = 90 c = 135.008 γ = 120
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 315r 2014-11-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97924 APS 19-ID
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 2.4 50 100 0.061 0.061 0.073 0.04 9.8 3.2 61899 -3 56.9
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 2.4 2.44 100 0.63 0.63 0.761 0.422 0.685 2 3.2
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 5J23 2.4 36.78 58425 2939 99.93 0.1381 0.1355 0.1386 0.1904 0.1934 RANDOM 57.536
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] -12.97 -12.97 25.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.688 r_dihedral_angle_4_deg 20.002 r_dihedral_angle_3_deg 13.657 r_dihedral_angle_1_deg 5.533 r_angle_refined_deg 1.319 r_angle_other_deg 1.132 r_chiral_restr 0.068 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.688 r_dihedral_angle_4_deg 20.002 r_dihedral_angle_3_deg 13.657 r_dihedral_angle_1_deg 5.533 r_angle_refined_deg 1.319 r_angle_other_deg 1.132 r_chiral_restr 0.068 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.005 r_gen_planes_other 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9325 Nucleic Acid Atoms Solvent Atoms 972 Heterogen Atoms 25
Software Software Software Name Purpose HKL-3000 data collection HKL-3000 data reduction HKL-3000 data scaling HKL-3000 phasing MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction