☰ Navigation Tabs
Crystal Structure of the CYP102A1 (P450BM3) Heme Domain with N-Hexadecanoyl-L-Homoserine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZO9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 293 9%(w/v) PEG8000, 59 mM Magnesium Chloride, 74 mM Tris-HCl, 128 uM N-Hexadecanoyl-L-Homoserine, 1.3%(v/v) Methanol
Crystal Properties Matthews coefficient Solvent content 2.55 51.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.677 α = 90 b = 145.51 β = 97.27 c = 62.934 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 EIGER X 16M 2020-02-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.000000 SPring-8 BL41XU
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 1.4 48.5 100 0.06 0.065 0.024 1 19.6 7.5 204864
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 1.4 1.42 100 1.224 1.317 0.483 0.561 7.4
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 1ZO9 1.4 45.59 194674 10139 99.96 0.1589 0.1579 0.1669 0.1767 0.1844 RANDOM 18.219
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] -0.57 -0.39 -0.04 0.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.687 r_dihedral_angle_4_deg 16.16 r_dihedral_angle_3_deg 11.506 r_dihedral_angle_1_deg 6.399 r_angle_refined_deg 1.597 r_angle_other_deg 1.487 r_chiral_restr 0.084 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.687 r_dihedral_angle_4_deg 16.16 r_dihedral_angle_3_deg 11.506 r_dihedral_angle_1_deg 6.399 r_angle_refined_deg 1.597 r_angle_other_deg 1.487 r_chiral_restr 0.084 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7294 Nucleic Acid Atoms Solvent Atoms 844 Heterogen Atoms 234
Software Software Software Name Purpose XDS data reduction Aimless data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction