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Crystal structure of NADPH-dependent glyoxylate/hydroxypyruvate reductase SMc04462 (SmGhrB) from Sinorhizobium meliloti in complex with citrate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5UOG PDB entry 5UOG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 289 0.2 uL of 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 + 0.2 uL MCSG Suite II condition #9 (0.1 M sodium citrate, pH 5.0, 20% w/v PEG6000), equilibrated against 1.5 M sodium chloride in a 96-well 3-drop crystallization plate (Swissci), incubated with 1/50 v/v 2 mg/mL chymotrypsin solution at 289 K for 3 hours prior to crystallization
Crystal Properties Matthews coefficient Solvent content 2.2 44.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.188 α = 90 b = 157.926 β = 110.74 c = 64.719 γ = 90
Symmetry Space Group P 1 21 1
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 2014-07-25 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 2.1 50 98.4 0.096 0.096 0.115 0.062 6.7 3.2 68211 -3 28
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 2.1 2.14 99.1 0.431 0.431 0.515 0.279 0.834 2.3 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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 5UOG 2.1 50 64518 3350 98.36 0.1662 0.1642 0.204 0.203 RANDOM 35.344
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] 0.95 -1.07 2.13 -1.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.347 r_dihedral_angle_4_deg 22.175 r_dihedral_angle_3_deg 12.873 r_dihedral_angle_1_deg 5.904 r_angle_refined_deg 1.464 r_angle_other_deg 0.978 r_chiral_restr 0.082 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.347 r_dihedral_angle_4_deg 22.175 r_dihedral_angle_3_deg 12.873 r_dihedral_angle_1_deg 5.904 r_angle_refined_deg 1.464 r_angle_other_deg 0.978 r_chiral_restr 0.082 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9315 Nucleic Acid Atoms Solvent Atoms 1151 Heterogen Atoms 28
Software Software Software Name Purpose MD2 data collection HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling