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Crystal structure of NADPH-dependent glyoxylate/hydroxypyruvate reductase SMc02828 (SmGhrA) from Sinorhizobium meliloti in apo form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4Z0P
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 289 0.2 ul of 12 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide and 0.5 mM TCEP were mixed with 0.2 ul of the MCSG suite I condition # 88 (0.1 M Sodium citrate pH=5.6, 20% v/v 2-Propanol, 20% w/v PEG 4000 ) and equilibrated against 1.5 M NaCl solution in 96 Well 3 drop Crystallization Plate (Swissci)
Crystal Properties Matthews coefficient Solvent content 3.66 66.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.592 α = 90 b = 128.592 β = 90 c = 122.847 γ = 90
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 2015-04-18 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 50 100 0.108 0.108 0.117 0.044 6.9 6.9 67353 -3 28.5
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 2.03 100 0.902 0.902 0.986 0.389 0.615 1.7 6.6
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 4Z0P 2 50 63691 3517 99.86 0.1482 0.1468 0.1742 0.169 RANDOM 44.268
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] -0.19 -0.19 0.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.372 r_dihedral_angle_4_deg 19.916 r_dihedral_angle_3_deg 11.181 r_dihedral_angle_1_deg 5.6 r_angle_refined_deg 1.369 r_angle_other_deg 0.927 r_chiral_restr 0.083 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.372 r_dihedral_angle_4_deg 19.916 r_dihedral_angle_3_deg 11.181 r_dihedral_angle_1_deg 5.6 r_angle_refined_deg 1.369 r_angle_other_deg 0.927 r_chiral_restr 0.083 r_bond_refined_d 0.011 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 3424 Nucleic Acid Atoms Solvent Atoms 659 Heterogen Atoms 13
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 DENZO data reduction SCALEPACK data scaling