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Structure of the partially unliganded met state of 400 kDa hemoglobin: Insights into ligand-induced structural changes of giant hemoglobins
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2D2M PDB ENTRY 2D2M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 7% PEG 10000, 0.2M Tris-HCl (pH 8.0), VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.64 53.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.96 α = 90 b = 110.96 β = 90 c = 271.58 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 90 CCD RIGAKU JUPITER 210 Rh-coated cylindrical bending mirror 2006-06-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B1 1.0000 SPring-8 BL26B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.95 50 99.7 0.061 32.8 9.2 47042 47042 -3 22.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2.02 99.4 0.337 5.8 7.2 4642
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2D2M 1.95 39.22 46892 2332 99.2 0.169 0.1637 0.202 0.1958 RANDOM 29.5
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] 4.57 4.57 -9.14
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 18.6 c_scangle_it 2.84 c_scbond_it 2.03 c_mcangle_it 1.84 c_angle_deg 1.3 c_mcbond_it 1.26 c_improper_angle_d 0.95 c_bond_d 0.01 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 18.6 c_scangle_it 2.84 c_scbond_it 2.03 c_mcangle_it 1.84 c_angle_deg 1.3 c_mcbond_it 1.26 c_improper_angle_d 0.95 c_bond_d 0.01 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4339 Nucleic Acid Atoms Solvent Atoms 523 Heterogen Atoms 186
Software Software Software Name Purpose CNS refinement BSS data collection HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing