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Crystal structure of dehydrosqualene synthase (crtm) from s. aureus complexed with bph-1183
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NPR PDB ENTRY 3NPR
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, PH 7.4, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K
Crystal Properties Matthews coefficient Solvent content 2.45 49.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.229 α = 90 b = 80.229 β = 90 c = 91.82 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) 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 2.07 50 99.9 21465 2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 3NPR 2.07 50 2 20136 1085 99.6 0.189 0.187 0.1871 0.223 0.2223 RANDOM 31.39
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] 0.1 0.05 0.1 -0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.982 r_dihedral_angle_4_deg 21.083 r_dihedral_angle_3_deg 15.85 r_scangle_it 5.853 r_dihedral_angle_1_deg 5.769 r_scbond_it 3.615 r_mcangle_it 2.203 r_angle_refined_deg 1.786 r_mcbond_it 1.164 r_chiral_restr 0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.982 r_dihedral_angle_4_deg 21.083 r_dihedral_angle_3_deg 15.85 r_scangle_it 5.853 r_dihedral_angle_1_deg 5.769 r_scbond_it 3.615 r_mcangle_it 2.203 r_angle_refined_deg 1.786 r_mcbond_it 1.164 r_chiral_restr 0.13 r_bond_refined_d 0.023 r_gen_planes_refined 0.009 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 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 175 Heterogen Atoms 32
Software Software Software Name Purpose PHASES phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling