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Crystal Structure of Citrate Synthase from Pyrobaculum aerophilum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VGP PDB ENTRY 1VGP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 297 20% PEG 8000, 0.1M Sodium cacodylate trihydrate pH 6.5, 0.2M Magnesium acetate tetrahydrate, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Crystal Properties Matthews coefficient Solvent content 2.28 45.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.418 α = 90 b = 89.803 β = 90 c = 146.331 γ = 90
Symmetry Space Group P 21 21 21
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 315 Mirrors 2005-12-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 1.00000 ALS 8.2.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.6 76.47 95.5 0.085 21.2 6.9 107121 107121 22.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.66 90.2 0.686 3.2 5.8 9959
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 PDB ENTRY 1VGP 1.6 76.47 100651 100651 5286 94.34 0.15929 0.15929 0.15769 0.1657 0.18975 0.1974 RANDOM 12.828
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 0.28 -0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.68 r_dihedral_angle_4_deg 11.106 r_dihedral_angle_3_deg 9.834 r_scangle_it 7.403 r_scbond_it 5.36 r_mcbond_it 4.306 r_mcangle_it 4.306 r_dihedral_angle_1_deg 3.303 r_angle_refined_deg 1.227 r_mcbond_other 0.968
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.68 r_dihedral_angle_4_deg 11.106 r_dihedral_angle_3_deg 9.834 r_scangle_it 7.403 r_scbond_it 5.36 r_mcbond_it 4.306 r_mcangle_it 4.306 r_dihedral_angle_1_deg 3.303 r_angle_refined_deg 1.227 r_mcbond_other 0.968 r_angle_other_deg 0.81 r_symmetry_vdw_other 0.282 r_nbd_refined 0.219 r_nbd_other 0.205 r_symmetry_hbond_refined 0.199 r_nbtor_refined 0.193 r_symmetry_vdw_refined 0.151 r_xyhbond_nbd_refined 0.149 r_metal_ion_refined 0.105 r_chiral_restr 0.093 r_nbtor_other 0.088 r_gen_planes_refined 0.009 r_bond_refined_d 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6528 Nucleic Acid Atoms Solvent Atoms 808 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement BOS data collection DENZO data reduction SCALEPACK data scaling PHASER phasing