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Crystal structure of the C(30) carotenoid dehydrosqualene synthase from Staphylococcus aureus complexed with intermediate PSPP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ZCO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 298 11-21% PEG 4000, 0.3-0.4M MgCl2, 0.1M Tris, 0.5 mM PSPP, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.46 49.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.685 α = 90 b = 80.685 β = 90 c = 90.794 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 ADSC QUANTUM 315 Vertically Collimating Premirror, Toroidal Focusing Mirror 2009-09-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13B1 1.0000 NSRRC BL13B1
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 1.89 30 99.9 0.031 49.4 7.3 27854 27821 1
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 1.89 1.96 100 0.323 5.2 7.5 2720
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 2ZCO 1.89 30 26389 1395 99.86 0.17071 0.1682 0.22236 0.2694 RANDOM 24.272
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] 1.05 0.52 1.05 -1.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.562 r_dihedral_angle_4_deg 19.908 r_dihedral_angle_3_deg 14.682 r_sphericity_free 6.974 r_dihedral_angle_1_deg 5.114 r_scangle_it 4.964 r_sphericity_bonded 3.652 r_scbond_it 3.324 r_rigid_bond_restr 2.225 r_mcangle_it 2.198
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.562 r_dihedral_angle_4_deg 19.908 r_dihedral_angle_3_deg 14.682 r_sphericity_free 6.974 r_dihedral_angle_1_deg 5.114 r_scangle_it 4.964 r_sphericity_bonded 3.652 r_scbond_it 3.324 r_rigid_bond_restr 2.225 r_mcangle_it 2.198 r_mcbond_it 1.383 r_angle_refined_deg 1.329 r_chiral_restr 0.091 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2385 Nucleic Acid Atoms Solvent Atoms 263 Heterogen Atoms 41
Software Software Software Name Purpose HKL-2000 data collection CNS refinement REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling CNS phasing