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Crystal structure of the human squalene synthase in complex with zaragozic acid A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EZF PDB ENTRY 1EZF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 2% PEG 400, 2M K2HPO4/NaH2PO4, 0.5mM zaragozic acid A, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.55 51.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.873 α = 90 b = 153.153 β = 91.72 c = 91.855 γ = 90
Symmetry Space Group P 1 21 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 Vertically Collimating Premirror, Toroidal Focusing Mirror 2009-07-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13B1 1.00000 NSRRC BL13B1
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 1.89 30 99.4 0.06 20.8 3.7 189042 187887 1 31.4
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 1.89 1.96 99.2 0.472 2.3 3.6 18909
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 1EZF 1.89 27.7 187819 9431 99.37 0.15035 0.14787 0.1485 0.19717 0.1985 RANDOM 38.25
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] -1.26 1.36 -0.39 1.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.251 r_dihedral_angle_4_deg 17.109 r_dihedral_angle_3_deg 14.552 r_scangle_it 5.026 r_dihedral_angle_1_deg 4.884 r_scbond_it 3.345 r_mcangle_it 2.083 r_rigid_bond_restr 1.723 r_angle_refined_deg 1.4 r_mcbond_it 1.246
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.251 r_dihedral_angle_4_deg 17.109 r_dihedral_angle_3_deg 14.552 r_scangle_it 5.026 r_dihedral_angle_1_deg 4.884 r_scbond_it 3.345 r_mcangle_it 2.083 r_rigid_bond_restr 1.723 r_angle_refined_deg 1.4 r_mcbond_it 1.246 r_chiral_restr 0.095 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 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 16139 Nucleic Acid Atoms Solvent Atoms 1390 Heterogen Atoms 326
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling