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Crystal structure of dehydrosqualene synthase (Crtm) from S. aureus complexed with quinuclidine BPH-651 in the S1 site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ZCO PDB ENTRY 2ZCO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 0.2M POTASSIUM SODIUM TARTRATE, 20% W/ V PEG 3350, 1MM PPI, 1MM BPH-651 (LIGAND), pH 7.4, VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 2.5 50.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.589 α = 90 b = 80.589 β = 90 c = 91.759 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 225 mm CCD 2010-07-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F APS 21-ID-F
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 2.06 50 99.9 0.073 12.7 21615 21594 2 2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 PDB ENTRY 2ZCO 2.06 30 2 20746 20373 1093 98.2 0.193 0.191 0.1903 0.241 0.2423 RANDOM 34
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] 0.37 0.18 0.37 -0.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.173 r_dihedral_angle_4_deg 17.626 r_dihedral_angle_3_deg 15.753 r_scangle_it 6.227 r_dihedral_angle_1_deg 5.794 r_scbond_it 3.948 r_mcangle_it 2.435 r_angle_refined_deg 1.331 r_mcbond_it 1.315 r_chiral_restr 0.115
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.173 r_dihedral_angle_4_deg 17.626 r_dihedral_angle_3_deg 15.753 r_scangle_it 6.227 r_dihedral_angle_1_deg 5.794 r_scbond_it 3.948 r_mcangle_it 2.435 r_angle_refined_deg 1.331 r_mcbond_it 1.315 r_chiral_restr 0.115 r_bond_refined_d 0.015 r_gen_planes_refined 0.012 r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2392 Nucleic Acid Atoms Solvent Atoms 184 Heterogen Atoms 21
Software Software Software Name Purpose PHASES phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling