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The crystal structure of haemoglobin from Atlantic cod
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model Other homology model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 298 0.1 M Bicine, pH 8.5, 12% PEGMME 5K
Crystal Properties Matthews coefficient Solvent content 2.51 51.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.691 α = 90 b = 103.257 β = 90 c = 199.352 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 X 6M 2016-09-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.91840 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.5 50 98.8 0.088 0.1 0.046 0.997 10.6 4.4 45021
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.59 97.3 0.809 0.917 0.419 0.597 4.4
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT homology model 2.5 50 42768 2191 98.28 0.2356 0.2323 0.3013 0.279 RANDOM 55.621
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] -1.49 -1.09 2.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.918 r_dihedral_angle_4_deg 19.775 r_dihedral_angle_3_deg 16.139 r_dihedral_angle_1_deg 6.284 r_angle_refined_deg 1.607 r_angle_other_deg 1.073 r_chiral_restr 0.108 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_gen_planes_other 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.918 r_dihedral_angle_4_deg 19.775 r_dihedral_angle_3_deg 16.139 r_dihedral_angle_1_deg 6.284 r_angle_refined_deg 1.607 r_angle_other_deg 1.073 r_chiral_restr 0.108 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_gen_planes_other 0.004 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8468 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 344
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing PDB_EXTRACT data extraction