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Cytochrome P450 reductase in complex with NADPH from Mycosarcoma maydis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6T1U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 289 0.1 M sodium citrate tribasic dihydrate pH 5.0, 30% (v/v) Jeffamine ED-2001 pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.41 49.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.533 α = 90 b = 139.027 β = 90 c = 153.593 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 80 PIXEL DECTRIS EIGER2 XE 16M 2023-03-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.99989 Diamond I04-1
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 2.45 76.92 99.8 0.408 0.429 0.131 0.93 6.1 11.8 57810
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 2.45 2.52 99.2 3.795 4.037 1.318 0.481 11.4
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.45 76.92 57711 2840 99.7 0.2033 0.2141 0.2424 0.2543 RANDOM 30.065
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] -0.65 -0.06 0.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.724 r_dihedral_angle_1_deg 7.324 r_scangle_it 5.286 r_scangle_other 5.286 r_mcangle_other 3.933 r_mcangle_it 3.932 r_scbond_other 3.243 r_scbond_it 3.242 r_dihedral_angle_2_deg 2.631 r_mcbond_it 2.472
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.724 r_dihedral_angle_1_deg 7.324 r_scangle_it 5.286 r_scangle_other 5.286 r_mcangle_other 3.933 r_mcangle_it 3.932 r_scbond_other 3.243 r_scbond_it 3.242 r_dihedral_angle_2_deg 2.631 r_mcbond_it 2.472 r_mcbond_other 2.472 r_angle_refined_deg 1.025 r_angle_other_deg 0.391 r_nbd_refined 0.191 r_nbd_other 0.191 r_nbtor_refined 0.172 r_xyhbond_nbd_refined 0.145 r_chiral_restr 0.113 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10592 Nucleic Acid Atoms Solvent Atoms 189 Heterogen Atoms 292
Software Software Software Name Purpose REFMAC refinement Aimless data scaling DIALS data reduction PHASER phasing PDB_EXTRACT data extraction