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Simvastatin Synthase (LovD), from Aspergillus terreus, S5 mutant, S76A mutant, complex with monacolin J acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HLD PDB entry 3HLD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 298 13% PEG 1000, 0.1M imidazole pH 8.0, 0.1 M calcium acetate, 10 mM dithiothreitol, vapor diffusion, hanging drop, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.02 59.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.062 α = 90 b = 75.321 β = 90 c = 133.026 γ = 90
Symmetry Space Group P 21 21 21
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 2009-03-29 SINGLE WAVELENGTH 2 1 x-ray 100 IMAGE PLATE RIGAKU HTC 2009-03-26 SINGLE WAVELENGTH 1,2 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.9792 APS 24-ID-C 2 ROTATING ANODE RIGAKU 1.5418
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 2.05 60 99.9 0.067 38.334 15.4 37141
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 2.05 2.12 99.8 0.443 12.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 FOURIER SYNTHESIS THROUGHOUT PDB entry 3HLD 2.06 49.86 37069 35223 1846 99.85 0.17829 0.1767 0.1895 0.20811 0.2136 RANDOM 41.683
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] 1.31 -0.8 -0.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.778 r_dihedral_angle_3_deg 14.329 r_dihedral_angle_4_deg 12.685 r_dihedral_angle_1_deg 5.887 r_angle_other_deg 4.081 r_scangle_it 3.442 r_mcangle_it 2.944 r_scbond_it 2.148 r_mcbond_it 1.877 r_angle_refined_deg 1.193
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.778 r_dihedral_angle_3_deg 14.329 r_dihedral_angle_4_deg 12.685 r_dihedral_angle_1_deg 5.887 r_angle_other_deg 4.081 r_scangle_it 3.442 r_mcangle_it 2.944 r_scbond_it 2.148 r_mcbond_it 1.877 r_angle_refined_deg 1.193 r_chiral_restr 0.069 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_gen_planes_other 0.005 r_bond_other_d 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 3313 Nucleic Acid Atoms Solvent Atoms 157 Heterogen Atoms 32
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction ADSC data collection