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Crystal structure of the C(30) carotenoid dehydrosqualene synthase from Staphylococcus aureus complexed with BPH-651
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 7.5 298 0.12-0.58M potassium sodium tartrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.44 49.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.66 α = 90 b = 80.66 β = 90 c = 90.216 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 2008-12-17 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 1.63 30 99.5 0.032 35.4 3.4 42844 42617 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 1.63 1.69 100 0.487 2.1 3.4 4208
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 2ZCO 1.63 30 40455 2149 99.49 0.17565 0.17416 0.2046 0.20336 0.2295 RANDOM 23.937
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] 0.6 0.3 0.6 -0.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.519 r_dihedral_angle_4_deg 18.146 r_dihedral_angle_3_deg 12.452 r_sphericity_free 6.871 r_scangle_it 5.454 r_dihedral_angle_1_deg 4.967 r_sphericity_bonded 3.985 r_scbond_it 3.667 r_mcangle_it 2.342 r_rigid_bond_restr 2.237
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.519 r_dihedral_angle_4_deg 18.146 r_dihedral_angle_3_deg 12.452 r_sphericity_free 6.871 r_scangle_it 5.454 r_dihedral_angle_1_deg 4.967 r_sphericity_bonded 3.985 r_scbond_it 3.667 r_mcangle_it 2.342 r_rigid_bond_restr 2.237 r_mcbond_it 1.494 r_angle_refined_deg 1.482 r_chiral_restr 0.1 r_gen_planes_refined 0.008 r_bond_refined_d 0.007 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 2392 Nucleic Acid Atoms Solvent Atoms 287 Heterogen Atoms 21
Software Software Software Name Purpose HKL-2000 data collection CNS refinement REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling CNS phasing