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Crystal structure of the human squalene synthase in complex with farnesyl thiopyrophosphate and magnesium ion
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3VJ8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 20% PEG 4000, 10% 2-propanol, 0.1M HEPES, 3mM farnesyl thiopyrophosphate, 1mM MgCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.14 42.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.369 α = 90 b = 106.721 β = 90 c = 33.569 γ = 90
Symmetry Space Group P 21 21 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 CCD ADSC QUANTUM 315r mirrors 2010-10-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 0.98000 Photon Factory BL-17A
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 1.75 30 99.3 0.088 27.5 5.9 35232 34977 1 28.4
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 1.75 1.81 99.1 0.523 3.3 4.6 3427
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 3VJ8 1.75 28.43 34777 1740 98.82 0.15773 0.15509 0.1534 0.20761 0.2068 RANDOM 25.516
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] -0.44 -1.47 1.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.437 r_dihedral_angle_4_deg 17.516 r_dihedral_angle_3_deg 13.536 r_scangle_it 5.61 r_dihedral_angle_1_deg 4.589 r_scbond_it 3.553 r_mcangle_it 2.326 r_rigid_bond_restr 1.722 r_angle_refined_deg 1.402 r_mcbond_it 1.335
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.437 r_dihedral_angle_4_deg 17.516 r_dihedral_angle_3_deg 13.536 r_scangle_it 5.61 r_dihedral_angle_1_deg 4.589 r_scbond_it 3.553 r_mcangle_it 2.326 r_rigid_bond_restr 1.722 r_angle_refined_deg 1.402 r_mcbond_it 1.335 r_chiral_restr 0.093 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2699 Nucleic Acid Atoms Solvent Atoms 283 Heterogen Atoms 51
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling