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Crystal structure of CYP116B46-N(20-445) from Tepidiphilus thermophilus in complex with HEME
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6GII
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.9 298 0.1M BICINE pH 8.5, 40% PEG1500 5% propanol
Crystal Properties Matthews coefficient Solvent content 2.15 42.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.471 α = 90 b = 75.511 β = 90 c = 105.148 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 CCD RAYONIX MX300-HS 2019-07-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE TPS 05A 0.9998 NSRRC TPS 05A
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 1.38 25 97.6 0.076 0.082 0.03 7.6 7.4 85629
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 1.38 1.43 91.5 0.436 0.475 0.185 0.904 5.9
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 6GII 1.38 24.52 81316 4241 97.42 0.1502 0.1489 0.1562 0.1732 0.1782 RANDOM 14.735
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] -0.7 1.06 -0.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.125 r_dihedral_angle_4_deg 15.078 r_dihedral_angle_3_deg 12.714 r_dihedral_angle_1_deg 6.658 r_angle_refined_deg 2.034 r_angle_other_deg 1.617 r_chiral_restr 0.102 r_bond_refined_d 0.014 r_gen_planes_refined 0.012 r_gen_planes_other 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.125 r_dihedral_angle_4_deg 15.078 r_dihedral_angle_3_deg 12.714 r_dihedral_angle_1_deg 6.658 r_angle_refined_deg 2.034 r_angle_other_deg 1.617 r_chiral_restr 0.102 r_bond_refined_d 0.014 r_gen_planes_refined 0.012 r_gen_planes_other 0.004 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3430 Nucleic Acid Atoms Solvent Atoms 654 Heterogen Atoms 60
Software Software Software Name Purpose HKL-2000 data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction PHASER phasing