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Structure determination of haemoglobin from Donkey(equus asinus) at 3.0 Angstrom resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2MHB Horse Methaemoglobin(PDB ID:2MHB)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.8 293 2.8M Na/K phosphate buffer, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.67 53.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.664 α = 90 b = 63.084 β = 111.75 c = 54.042 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 298 IMAGE PLATE MARRESEARCH Monochromator 2003-10-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 3.002 30 79.01 0.161 4.3 4.1 5406 5387 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 3.002 3.079 34.3 0.43 584
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 Horse Methaemoglobin(PDB ID:2MHB) 3 21.18 2 5387 5133 254 79.01 0.1857 0.1857 0.18072 0.1923 0.28524 0.2832 RANDOM 33.322
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] -0.11 -0.12 -0.04 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 11.291 r_scangle_it 5.571 r_scbond_it 3.22 r_angle_refined_deg 3.149 r_mcangle_it 2.321 r_angle_other_deg 1.512 r_mcbond_it 1.218 r_symmetry_vdw_refined 0.306 r_nbd_refined 0.293 r_symmetry_vdw_other 0.292
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 11.291 r_scangle_it 5.571 r_scbond_it 3.22 r_angle_refined_deg 3.149 r_mcangle_it 2.321 r_angle_other_deg 1.512 r_mcbond_it 1.218 r_symmetry_vdw_refined 0.306 r_nbd_refined 0.293 r_symmetry_vdw_other 0.292 r_nbd_other 0.285 r_xyhbond_nbd_refined 0.21 r_chiral_restr 0.131 r_nbtor_other 0.12 r_symmetry_hbond_refined 0.057 r_bond_refined_d 0.041 r_gen_planes_refined 0.01 r_gen_planes_other 0.005 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2200 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 86
Software Software Software Name Purpose REFMAC refinement MAR345 data collection SCALEPACK data scaling AMoRE phasing