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Crystal structure of citrate synthase (Msed_1522) from Metallosphaera sedula in complex with citrate
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 4.2 295 800mM sodium phosphate monobasic/1200mM potassium phosphate dibasic, 0.1 M sodium acetate/acetic acid pH 4.2
Crystal Properties Matthews coefficient Solvent content 2.21 44.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.181 α = 93.56 b = 53.522 β = 105.73 c = 76.285 γ = 102.16
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 2017-10-15 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) 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 72.84 97.1 0.057 22 3.5 79198
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.73 0.263
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 1.7 29.15 75282 3916 96.77 0.1461 0.1443 0.1581 0.1803 0.1933 RANDOM 21.068
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] -0.2 0.89 0.11 0.68 0.43 -0.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.459 r_dihedral_angle_4_deg 19.468 r_dihedral_angle_3_deg 14.261 r_dihedral_angle_1_deg 5.987 r_angle_refined_deg 1.688 r_angle_other_deg 1.082 r_chiral_restr 0.162 r_bond_refined_d 0.014 r_gen_planes_refined 0.009 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.459 r_dihedral_angle_4_deg 19.468 r_dihedral_angle_3_deg 14.261 r_dihedral_angle_1_deg 5.987 r_angle_refined_deg 1.688 r_angle_other_deg 1.082 r_chiral_restr 0.162 r_bond_refined_d 0.014 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5918 Nucleic Acid Atoms Solvent Atoms 593 Heterogen Atoms 44
Software Software Software Name Purpose HKL-2000 data reduction REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data scaling MOLREP phasing