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The BM3 mutant WIFI-WC heme domain in complex with testosterone
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JPZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 297 25% w/v PEG 550 MME, 0.1 M MES pH 6.5, 0.01 M zinc sulfate heptahydrate
Crystal Properties Matthews coefficient Solvent content 2.4 48.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.39 α = 90 b = 89.502 β = 90 c = 172.55 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 PILATUS3 R CdTe 300K-W 2015-11-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.979 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.09 29.64 99 0.075 0.999 14.7 6.7 62142
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.09 2.14 97.3 0.731 0.786 2.4 6.7
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 1JPZ 2.09 29.64 58933 3155 98.83 0.19504 0.19263 0.1987 0.23865 0.2426 RANDOM 44.692
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] -0.05 -0.06 0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.541 r_dihedral_angle_3_deg 16.793 r_dihedral_angle_4_deg 14.064 r_dihedral_angle_1_deg 6.225 r_angle_refined_deg 1.768 r_angle_other_deg 1.164 r_chiral_restr 0.122 r_bond_refined_d 0.015 r_gen_planes_refined 0.009 r_gen_planes_other 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.541 r_dihedral_angle_3_deg 16.793 r_dihedral_angle_4_deg 14.064 r_dihedral_angle_1_deg 6.225 r_angle_refined_deg 1.768 r_angle_other_deg 1.164 r_chiral_restr 0.122 r_bond_refined_d 0.015 r_gen_planes_refined 0.009 r_gen_planes_other 0.006 r_bond_other_d 0.005 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_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 7309 Nucleic Acid Atoms Solvent Atoms 468 Heterogen Atoms 172
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling Coot model building