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Crystal structure of NADPH-dependent glyoxylate/hydroxypyruvate reductase SMc04462 (SmGhrB) from Sinorhizobium meliloti in complex with NADP and malonate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5J23 PDB entry 5J23
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 289 0.2 uL 13 mg/mL protein in 20 mM HEPES, pH 7.5, 150 mM sodium chloride, 10% glycerol, 0.1% sodium azide, 0.5 mM TCEP, 5 mM NADP + 0.2 uL MCSG Suite II condition #20 (1.1 M malonic acid, 0.072 M succinic acid, 0.15 M ammonium citrate tribasic, 0.18 M DL-malic acid, 0.096 M ammonium tartrate dibasic, 0.24 M sodium acetate, 0.3 M sodium formate, pH 7), equilibrated against 1.5 M sodium chloride in a 96-well, 3-drop crystallization plate (Swissci), incubated with 1/50 v/v 1 mg/mL rTEV at 289 K for 3 hours prior to crystallization
Crystal Properties Matthews coefficient Solvent content 2.96 58.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 176.484 α = 90 b = 176.484 β = 90 c = 135.857 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 MARMOSAIC 300 mm CCD Beryllium Lenses 2014-07-24 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) 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 1.95 50 99.6 0.105 0.105 0.119 0.055 7.6 4.6 114355 -3 30
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 1.95 1.98 98.6 0.691 0.691 0.784 0.366 0.686 2.1 4.5 5653
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 PDB entry 5J23 1.95 40.29 108794 5559 99.54 0.1444 0.1438 0.1486 0.1565 0.1592 RANDOM 33.875
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] -2.22 -2.22 4.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.507 r_dihedral_angle_4_deg 20.3 r_dihedral_angle_3_deg 11.866 r_dihedral_angle_1_deg 5.94 r_angle_refined_deg 1.34 r_angle_other_deg 1.1 r_chiral_restr 0.069 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.507 r_dihedral_angle_4_deg 20.3 r_dihedral_angle_3_deg 11.866 r_dihedral_angle_1_deg 5.94 r_angle_refined_deg 1.34 r_angle_other_deg 1.1 r_chiral_restr 0.069 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.004 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9446 Nucleic Acid Atoms Solvent Atoms 841 Heterogen Atoms 223
Software Software Software Name Purpose MD2 data collection HKL-3000 data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction DENZO data reduction SCALEPACK data scaling