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Crystal structure of the Y248A mutant of C(30) carotenoid dehydrosqualene synthase from Staphylococcus aureus in complex with zaragozic acid A
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 8.5 298 11-21% PEG 4000, 0.3-0.4M MgCl2, 0.1M Tris pH 8.5, 0.25mM zaragozic acid A, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.48 50.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.177 α = 90 b = 80.177 β = 90 c = 185.414 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 RAYONIX MX225HE HORIZONTAL FOCUSING MIRROR 2010-07-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.90000 SPring-8 BL44XU
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 2.12 30 99.5 0.071 33.6 9 40047 39844 1 50.3
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 2.12 2.2 99.9 0.485 4.8 9 3912
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 PDB ENTRY 2ZCO 2.12 28.3 39655 1992 99.22 0.20764 0.20509 0.2031 0.25401 0.2543 RANDOM 48.162
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] 0.69 0.34 0.69 -1.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.845 r_dihedral_angle_3_deg 16.7 r_dihedral_angle_4_deg 16.666 r_dihedral_angle_1_deg 5.472 r_scangle_it 4.528 r_scbond_it 2.835 r_mcangle_it 2.053 r_rigid_bond_restr 1.424 r_angle_refined_deg 1.396 r_mcbond_it 1.131
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.845 r_dihedral_angle_3_deg 16.7 r_dihedral_angle_4_deg 16.666 r_dihedral_angle_1_deg 5.472 r_scangle_it 4.528 r_scbond_it 2.835 r_mcangle_it 2.053 r_rigid_bond_restr 1.424 r_angle_refined_deg 1.396 r_mcbond_it 1.131 r_chiral_restr 0.103 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 r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4770 Nucleic Acid Atoms Solvent Atoms 167 Heterogen Atoms 98
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling