☰ Navigation Tabs
Crystal structure of the C(30) carotenoid dehydrosqualene synthase from Staphylococcus aureus complexed with geranylgeranyl thiopyrophosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ZCP
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, 0.5mM GGsPP, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.45 49.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.118 α = 90 b = 80.118 β = 90 c = 183.617 γ = 120
Symmetry Space Group P 31 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 315r mirrors 2009-11-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0000 Photon Factory BL-5A
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 2.37 30 99.1 0.056 32.5 6.2 28590 28335 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 2.37 2.45 97.5 0.581 3.1 5.7 2767
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 2ZCP 2.37 30 26857 1428 98.98 0.22234 0.21925 0.2601 0.28055 0.3063 RANDOM 31.492
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] 1.64 0.82 1.64 -2.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.015 r_dihedral_angle_3_deg 19.007 r_dihedral_angle_4_deg 14.831 r_sphericity_free 9.735 r_dihedral_angle_1_deg 5.544 r_scangle_it 4.715 r_sphericity_bonded 3.154 r_scbond_it 3.108 r_mcangle_it 2.18 r_rigid_bond_restr 2.122
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.015 r_dihedral_angle_3_deg 19.007 r_dihedral_angle_4_deg 14.831 r_sphericity_free 9.735 r_dihedral_angle_1_deg 5.544 r_scangle_it 4.715 r_sphericity_bonded 3.154 r_scbond_it 3.108 r_mcangle_it 2.18 r_rigid_bond_restr 2.122 r_angle_refined_deg 1.522 r_mcbond_it 1.262 r_chiral_restr 0.105 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 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 4772 Nucleic Acid Atoms Solvent Atoms 70 Heterogen Atoms 122
Software Software Software Name Purpose HKL-2000 data collection CNS refinement REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling CNS phasing