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Hemoglobin Dodecamer from Lumbricus Erythrocruorin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other 3.8A in-house structure of full erythrocruorin
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.8 281 2.8M Na phosphate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 281.0K
Crystal Properties Matthews coefficient Solvent content 2.92 57.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 139.225 α = 90 b = 172.071 β = 90 c = 202.886 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray IMAGE PLATE RIGAKU RAXIS IIC M SINGLE WAVELENGTH 2 1 x-ray CCD ADSC QUANTUM 4 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200H 1.5418 2 SYNCHROTRON APS BEAMLINE 14-BM-C 1.0000 APS 14-BM-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1,2 2.6 105.41 74920 74920
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3.8 Structure of the whole molecule 2.6 105.41 74920 63085 3337 88.66 0.21481 0.21481 0.21316 0.2133 0.24615 RANDOM 34.318
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] -1.45 -0.87 2.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.027 r_dihedral_angle_4_deg 22.066 r_dihedral_angle_3_deg 17.11 r_dihedral_angle_1_deg 4.236 r_angle_refined_deg 1.875 r_nbtor_refined 0.304 r_nbd_refined 0.297 r_symmetry_vdw_refined 0.287 r_metal_ion_refined 0.201 r_symmetry_hbond_refined 0.201
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.027 r_dihedral_angle_4_deg 22.066 r_dihedral_angle_3_deg 17.11 r_dihedral_angle_1_deg 4.236 r_angle_refined_deg 1.875 r_nbtor_refined 0.304 r_nbd_refined 0.297 r_symmetry_vdw_refined 0.287 r_metal_ion_refined 0.201 r_symmetry_hbond_refined 0.201 r_xyhbond_nbd_refined 0.131 r_chiral_restr 0.083 r_bond_refined_d 0.009 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14028 Nucleic Acid Atoms Solvent Atoms 264 Heterogen Atoms 555
Software Software Software Name Purpose REFMAC refinement CNS refinement SCALEPACK data scaling CNS phasing