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Crystal structure of CYP154E1 from Thermobifida fusca YX in complex with 4-Phenylimidazole
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ODO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 0.1 M HEPES pH 7.5, 20 % Polyethylene glycol 8000
Crystal Properties Matthews coefficient Solvent content 2.34 47.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.334 α = 90 b = 97.176 β = 90 c = 135.688 γ = 90
Symmetry Space Group P 21 21 21
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 2021-08-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.03319 PETRA III, DESY P11
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 2 48.984 99.7 0.224 0.242 0.092 0.998 9.3 13 56184
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 2 2.05 2.09 2.272 0.882 0.475 1.2 12.4
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 NONE 2.002 48.984 56072 2787 99.618 0.221 0.2184 0.219 0.2714 0.271 34.445
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] 1.023 -0.454 -0.569
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.217 r_dihedral_angle_3_deg 14.034 r_dihedral_angle_2_deg 12.395 r_dihedral_angle_1_deg 7.982 r_lrange_it 6.968 r_lrange_other 6.965 r_scangle_it 5.616 r_scangle_other 5.616 r_mcangle_it 4.374 r_mcangle_other 4.374
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.217 r_dihedral_angle_3_deg 14.034 r_dihedral_angle_2_deg 12.395 r_dihedral_angle_1_deg 7.982 r_lrange_it 6.968 r_lrange_other 6.965 r_scangle_it 5.616 r_scangle_other 5.616 r_mcangle_it 4.374 r_mcangle_other 4.374 r_scbond_it 3.82 r_scbond_other 3.819 r_mcbond_it 3.183 r_mcbond_other 3.183 r_angle_refined_deg 1.741 r_angle_other_deg 0.595 r_nbd_other 0.238 r_nbd_refined 0.221 r_symmetry_nbd_other 0.197 r_nbtor_refined 0.172 r_symmetry_nbd_refined 0.153 r_xyhbond_nbd_refined 0.152 r_symmetry_xyhbond_nbd_refined 0.151 r_ncsr_local_group_1 0.115 r_chiral_restr 0.086 r_metal_ion_refined 0.085 r_symmetry_nbtor_other 0.08 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6172 Nucleic Acid Atoms Solvent Atoms 260 Heterogen Atoms 108
Software Software Software Name Purpose Aimless data scaling REFMAC refinement MOLREP phasing Coot model building XDS data reduction BUCCANEER model building