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Crystal structure of NADPH-dependent glyoxylate/hydroxypyruvate reductase SMc02828 (SmGhrA) from Sinorhizobium meliloti in complex with NADPH and oxalate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4WEQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7 289 0.2 ul of 12 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide, 0.5 mM TCEP, 5 mM NADPH, and 50 mM oxalic acid pH=7.0 were mixed with 0.2 ul of the MCSG Suite 2 condition #28 (0.2M Ammonium Citrate Tribasic, anhydrous, 20%w/v PEG 3350 pH=7) and equilibrated against 1.5 M NaCl solution in 96 Well 3 drop. Before crystallization, the protein-ligand mixture was incubated with 1/15 v/v of 1 mg/ml rTEV solution at 289 K for 3 hours
Crystal Properties Matthews coefficient Solvent content 3.93 68.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.099 α = 90 b = 108.099 β = 90 c = 80.226 γ = 120
Symmetry Space Group P 32 2 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 2014-11-06 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 1.7 50 99.9 0.074 0.074 0.069 0.031 8.3 6.9 60027 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.73 100 0.852 0.938 0.43 0.726 2.4 6.7 2901
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 4WEQ 1.7 50 56748 2954 99.93 0.1351 0.1344 0.146 0.1497 0.1585 RANDOM 31.028
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] 0.39 0.2 0.39 -1.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.518 r_dihedral_angle_4_deg 13.376 r_dihedral_angle_3_deg 11.034 r_dihedral_angle_1_deg 5.64 r_mcangle_it 3.826 r_mcbond_it 3.119 r_mcbond_other 3.116 r_angle_refined_deg 1.475 r_angle_other_deg 0.946 r_chiral_restr 0.088
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.518 r_dihedral_angle_4_deg 13.376 r_dihedral_angle_3_deg 11.034 r_dihedral_angle_1_deg 5.64 r_mcangle_it 3.826 r_mcbond_it 3.119 r_mcbond_other 3.116 r_angle_refined_deg 1.475 r_angle_other_deg 0.946 r_chiral_restr 0.088 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2404 Nucleic Acid Atoms Solvent Atoms 429 Heterogen Atoms 83
Software Software Software Name Purpose HKL-3000 data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data collection BLU-MAX data collection HKL-3000 phasing MOLREP phasing HKL-3000 data reduction