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Crystal structure of citrate synthase (Msed_1522) from Metallosphaera sedula in complex with oxaloacetate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VGP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295 22% polyethylene glycol (PEG) 3350 0.2M, potassium sodium tartrate tetrahydrate
Crystal Properties Matthews coefficient Solvent content 2.28 46.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.134 α = 83.73 b = 55.973 β = 73.94 c = 76.965 γ = 72.22
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 270 2018-05-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 0.97934 PAL/PLS 7A (6B, 6C1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 97.9 0.075 0.088 0.045 13.4 3.6 50558
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 2 2.03 96.6 0.281 0.333 0.177 0.9 3.4
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 1VGP 2 33.35 48053 2505 97.6 0.1499 0.1478 0.1578 0.1928 0.199 RANDOM 30.323
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] -0.15 -1.49 -0.47 0.83 0.86 -1.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.695 r_dihedral_angle_4_deg 19.282 r_dihedral_angle_3_deg 15.417 r_dihedral_angle_1_deg 6.215 r_angle_refined_deg 1.635 r_angle_other_deg 1.399 r_chiral_restr 0.082 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.695 r_dihedral_angle_4_deg 19.282 r_dihedral_angle_3_deg 15.417 r_dihedral_angle_1_deg 6.215 r_angle_refined_deg 1.635 r_angle_other_deg 1.399 r_chiral_restr 0.082 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5942 Nucleic Acid Atoms Solvent Atoms 328 Heterogen Atoms 88
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction PDB_EXTRACT data extraction HKL-2000 data scaling MOLREP phasing