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Globin sensor domain of AfGcHK (FeIII form) in complex with cyanide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2W31
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.7 298 20.7% (w/v) PEG3350, 200 mM MgCl2, 0.01 M KCN, 7.5% (v/v) glycerol, 0.1 M MMT buffer system (DL-Malic acid, MES monohydrate, Tris, NaOH, HCl), pH 6.7
Crystal Properties Matthews coefficient Solvent content 2.27 46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.069 α = 90 b = 78.069 β = 90 c = 441.819 γ = 90
Symmetry Space Group P 41 21 2
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 6M 2016-05-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.918409 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.85 46.82 100 0.139 0.059 0.998 11.1 11.9 118539 -3.7 14.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.88 100 1.157 0.517 0.804 1.9 10.9
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 2W31 1.85 46.82 118348 5826 99.98 0.19438 0.19242 0.202 0.24133 0.2047 Random selection 24
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 0.7 -1.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.145 r_dihedral_angle_4_deg 20.35 r_dihedral_angle_3_deg 15.262 r_long_range_B_refined 5.324 r_dihedral_angle_1_deg 5.097 r_long_range_B_other 5.025 r_scangle_other 3.328 r_mcangle_it 2.557 r_mcangle_other 2.557 r_scbond_it 2.113
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.145 r_dihedral_angle_4_deg 20.35 r_dihedral_angle_3_deg 15.262 r_long_range_B_refined 5.324 r_dihedral_angle_1_deg 5.097 r_long_range_B_other 5.025 r_scangle_other 3.328 r_mcangle_it 2.557 r_mcangle_other 2.557 r_scbond_it 2.113 r_scbond_other 2.112 r_mcbond_it 1.687 r_mcbond_other 1.684 r_angle_refined_deg 1.628 r_angle_other_deg 1.071 r_chiral_restr 0.125 r_bond_refined_d 0.014 r_gen_planes_refined 0.009 r_gen_planes_other 0.005 r_bond_other_d 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9891 Nucleic Acid Atoms Solvent Atoms 1117 Heterogen Atoms 361
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MoRDa phasing