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Structure of the BM3 heme domain in complex with clotrimazole
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4KF2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 PEG, 5mM ligand (dissolved in 100% DMSO), 25mM potassium phosphate, pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.8 56.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.408 α = 90 b = 70.747 β = 95.31 c = 209.644 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 PILATUS 300K 2017-02-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.98 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 2.08 100 91.7 0.08 1 11.8 3.4 121655
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.08 2.12 98.9 0.591 0.8 2.2 3.4
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 4KF2 2.08 48.32 121655 6344 91.62 0.16877 0.16681 0.1738 0.20672 0.2148 RANDOM 36.173
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] 0.37 0.17 0.88 -1.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.015 r_dihedral_angle_4_deg 16.29 r_dihedral_angle_3_deg 13.263 r_dihedral_angle_1_deg 6.004 r_angle_refined_deg 1.569 r_angle_other_deg 1.389 r_chiral_restr 0.163 r_bond_refined_d 0.016 r_gen_planes_refined 0.01 r_bond_other_d 0.009
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.015 r_dihedral_angle_4_deg 16.29 r_dihedral_angle_3_deg 13.263 r_dihedral_angle_1_deg 6.004 r_angle_refined_deg 1.569 r_angle_other_deg 1.389 r_chiral_restr 0.163 r_bond_refined_d 0.016 r_gen_planes_refined 0.01 r_bond_other_d 0.009 r_gen_planes_other 0.009 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 14701 Nucleic Acid Atoms Solvent Atoms 1097 Heterogen Atoms 465
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing