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Crystal structure of 3-hydroxy-3-methylglutaryl-coenzyme A synthase from Staphylococcus aureus
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 295 TRIS, ammonium sulfate, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.7 54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 119.401 α = 90 b = 119.401 β = 90 c = 114.115 γ = 120
Symmetry Space Group P 64 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV 2000-09-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 99 98 0.048 15.7 5.5 32374 2 23.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.07 95 0.27 6.5 5.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) 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 MIR THROUGHOUT 2 20 2 4 33021 29725 1577 95.08 0.16679 0.16546 0.1712 0.19144 0.191 RANDOM 22.907
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] -0.12 -0.06 -0.12 0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.694 r_scangle_it 3.496 r_scbond_it 2.171 r_angle_refined_deg 1.337 r_mcangle_it 1.213 r_mcbond_it 0.631 r_nbd_refined 0.212 r_symmetry_vdw_refined 0.179 r_symmetry_hbond_refined 0.153 r_xyhbond_nbd_refined 0.117
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.694 r_scangle_it 3.496 r_scbond_it 2.171 r_angle_refined_deg 1.337 r_mcangle_it 1.213 r_mcbond_it 0.631 r_nbd_refined 0.212 r_symmetry_vdw_refined 0.179 r_symmetry_hbond_refined 0.153 r_xyhbond_nbd_refined 0.117 r_chiral_restr 0.099 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_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 3040 Nucleic Acid Atoms Solvent Atoms 198 Heterogen Atoms 5
Software Software Software Name Purpose HKL-2000 data collection SCALEPACK data scaling MLPHARE phasing REFMAC refinement HKL-2000 data reduction