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Globin sensor domain of AfGcHK (FeIII form) in complex with cyanide, partially reduced
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5OHE
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 = 77.685 α = 90 b = 77.685 β = 90 c = 441.238 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 2015-09-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 1.000 PETRA III, EMBL c/o DESY P13 (MX1)
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 1.8 49.17 100 0.059 0.034 0.993 16.7 7.3 127077 -3.7 21
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 1.8 1.83 100 0.761 0.442 0.844 2.7 7.6
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 5OHE 1.8 49.17 126873 6224 99.98 0.19172 0.18991 0.1996 0.23867 0.2057 Random selection 28
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] 0.59 0.59 -1.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.001 r_dihedral_angle_4_deg 18.833 r_dihedral_angle_3_deg 14.257 r_long_range_B_refined 4.982 r_long_range_B_other 4.832 r_dihedral_angle_1_deg 4.32 r_scangle_other 3.089 r_mcangle_it 2.239 r_mcangle_other 2.239 r_scbond_it 1.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.001 r_dihedral_angle_4_deg 18.833 r_dihedral_angle_3_deg 14.257 r_long_range_B_refined 4.982 r_long_range_B_other 4.832 r_dihedral_angle_1_deg 4.32 r_scangle_other 3.089 r_mcangle_it 2.239 r_mcangle_other 2.239 r_scbond_it 1.89 r_scbond_other 1.889 r_mcbond_it 1.441 r_mcbond_other 1.439 r_angle_refined_deg 1.267 r_angle_other_deg 0.934 r_chiral_restr 0.103 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 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 9821 Nucleic Acid Atoms Solvent Atoms 1016 Heterogen Atoms 366
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling