☰ Navigation Tabs
Globin sensor domain of AfGcHK in monomeric form, with imidazole
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5OHF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 294 C4 Morpheus condition (0.09M NPS ligand stock (NaNO3, Na2HPO4, (NH4)2SO4), 0.1M buffer system pH 6.5 (imidazole, MES) and 37.5% precipitant stock MPD_P1K_P3350 (MPD, PEG 1000 and PEG 3350)
Crystal Properties Matthews coefficient Solvent content 2.2 43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.44 α = 90 b = 69.44 β = 90 c = 113.364 γ = 120
Symmetry Space Group P 61 2 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-F 2015-11-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.97 Diamond I02
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 41.25 99.2 0.073 0.028 0.999 18.3 13.9 15414 -3.7 29
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 1.84 99.9 1.32 0.506 0.703 14.2
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 5OHF 1.8 41.25 15412 754 98.66 0.18588 0.182 0.1949 0.231 0.2051 random selection 35.201
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] -0.69 -0.34 -0.69 2.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.886 r_dihedral_angle_4_deg 18.874 r_dihedral_angle_3_deg 15.375 r_long_range_B_refined 7.571 r_long_range_B_other 7.561 r_scangle_other 5.836 r_dihedral_angle_1_deg 4.623 r_scbond_it 3.739 r_scbond_other 3.737 r_mcangle_it 3.714
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.886 r_dihedral_angle_4_deg 18.874 r_dihedral_angle_3_deg 15.375 r_long_range_B_refined 7.571 r_long_range_B_other 7.561 r_scangle_other 5.836 r_dihedral_angle_1_deg 4.623 r_scbond_it 3.739 r_scbond_other 3.737 r_mcangle_it 3.714 r_mcangle_other 3.712 r_mcbond_it 2.726 r_mcbond_other 2.721 r_angle_refined_deg 1.7 r_angle_other_deg 1.054 r_chiral_restr 0.133 r_bond_refined_d 0.017 r_gen_planes_refined 0.01 r_gen_planes_other 0.007 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 1243 Nucleic Acid Atoms Solvent Atoms 68 Heterogen Atoms 61
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing