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Crystal structure of the human squalene synthase
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 8.5 298 20% PEG 2000 MME, 0.01M NiCl2, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.09 41.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.008 α = 90 b = 82.341 β = 91.57 c = 77.175 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 210 Vertically Collimating Premirror, Toroidal Focusing Mirror 2008-07-25 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 1.76 30 98.3 0.061 25.3 4.9 63922 62838 1 35
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 1.76 1.83 97.8 0.489 3.8 4.8 6313
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 1.76 24.5 62784 3180 98.08 0.16838 0.16483 0.1649 0.23304 0.2329 RANDOM 31.711
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] -0.25 -1.21 -0.02 0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.948 r_dihedral_angle_4_deg 17.981 r_dihedral_angle_3_deg 15.014 r_dihedral_angle_1_deg 5.275 r_scangle_it 5.156 r_scbond_it 3.34 r_mcangle_it 2.018 r_rigid_bond_restr 1.593 r_angle_refined_deg 1.393 r_mcbond_it 1.186
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.948 r_dihedral_angle_4_deg 17.981 r_dihedral_angle_3_deg 15.014 r_dihedral_angle_1_deg 5.275 r_scangle_it 5.156 r_scbond_it 3.34 r_mcangle_it 2.018 r_rigid_bond_restr 1.593 r_angle_refined_deg 1.393 r_mcbond_it 1.186 r_chiral_restr 0.098 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 5404 Nucleic Acid Atoms Solvent Atoms 568 Heterogen Atoms 2
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling