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Crystal structure of a dehydrosqualene synthase in complex with ligand
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4E9U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 298 24% PEG 3350, 0.1M Li2SO4, 0.1M Bis-Tris pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.11 41.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.238 α = 90 b = 41.09 β = 96.35 c = 93.477 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 2015-11-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13C1 1.0 NSRRC BL13C1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.93 25 98 0.064 0.076 0.04 13.7 3.3 21148
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 1.93 2 97.1 0.258 3.3
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 4E9U 1.93 25 20009 1088 97.45 0.1669 0.1641 0.165 0.2195 0.2177 RANDOM 29.324
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] 0.24 -0.66 -0.85 0.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.417 r_dihedral_angle_4_deg 20.969 r_dihedral_angle_3_deg 15.951 r_scangle_it 7.511 r_dihedral_angle_1_deg 6.085 r_scbond_it 4.894 r_mcangle_it 2.801 r_mcbond_it 1.76 r_angle_refined_deg 1.445 r_chiral_restr 0.111
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.417 r_dihedral_angle_4_deg 20.969 r_dihedral_angle_3_deg 15.951 r_scangle_it 7.511 r_dihedral_angle_1_deg 6.085 r_scbond_it 4.894 r_mcangle_it 2.801 r_mcbond_it 1.76 r_angle_refined_deg 1.445 r_chiral_restr 0.111 r_gen_planes_refined 0.017 r_bond_refined_d 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2325 Nucleic Acid Atoms Solvent Atoms 203 Heterogen Atoms 61
Software Software Software Name Purpose HKL-2000 data collection HKL-2000 data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction PHASER phasing