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Crystal Structure of a Squalene-Hopene Cyclase from Cystobacter fuscus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model RoseTTAFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 8.5 292 0.1 M Bicine/Trizma base pH 8.5, 0.03 M MgCl2, 0.03 M CaCl2, 12.5% PEG 1000, 12.5% PEG 3350, 12.5% MPD
Crystal Properties Matthews coefficient Solvent content 2.12 41.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.244 α = 90 b = 75.872 β = 94.269 c = 91.742 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 PIXEL DECTRIS EIGER2 X 16M 2021-07-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97628 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.42 58.42 97.89 0.129 0.142 0.057 0.993 6.9 6.4 121895
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.42 1.44 95.59 1.877 2.035 0.776 0.343 0.5 7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.42 45.785 121524 6103 97.838 0.168 0.1661 0.1946 0.2049 0.2253 13.039
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] 2.342 0.029 -0.762 -1.567
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.524 r_dihedral_angle_3_deg 13.462 r_dihedral_angle_2_deg 7.992 r_dihedral_angle_1_deg 5.846 r_rigid_bond_restr 3.381 r_lrange_it 2.126 r_lrange_other 1.956 r_angle_refined_deg 1.513 r_mcangle_it 1.203 r_mcangle_other 1.203
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.524 r_dihedral_angle_3_deg 13.462 r_dihedral_angle_2_deg 7.992 r_dihedral_angle_1_deg 5.846 r_rigid_bond_restr 3.381 r_lrange_it 2.126 r_lrange_other 1.956 r_angle_refined_deg 1.513 r_mcangle_it 1.203 r_mcangle_other 1.203 r_scangle_it 1.182 r_scangle_other 1.182 r_mcbond_it 0.845 r_mcbond_other 0.844 r_scbond_it 0.844 r_scbond_other 0.844 r_angle_other_deg 0.638 r_nbd_refined 0.222 r_symmetry_nbd_refined 0.187 r_nbd_other 0.186 r_symmetry_xyhbond_nbd_refined 0.184 r_nbtor_refined 0.181 r_symmetry_nbd_other 0.173 r_xyhbond_nbd_refined 0.131 r_ncsr_local_group_1 0.129 r_chiral_restr 0.086 r_symmetry_nbtor_other 0.071 r_symmetry_xyhbond_nbd_other 0.057 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_bond_other_d 0.003 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5371 Nucleic Acid Atoms Solvent Atoms 714 Heterogen Atoms 54
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling MrBUMP phasing