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Human hemoglobin, nitrogen dioxide anion modified
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1IRD PDB Entry 1IRD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIQUID DIFFUSION 6.8 295 Sodium phosphate, Potassium phosphate, Toluene, Hemoglobin, pH 6.8, LIQUID DIFFUSION, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.21 44.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.538 α = 90 b = 53.538 β = 90 c = 191.77 γ = 90
Symmetry Space Group P 41 21 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 IMAGE PLATE RIGAKU RAXIS IV Osmic 2008-05-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R 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 1.8 16.37 99.8 0.082 10.2 7.74 26808 26808 2 2 36.6
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) 1.8 1.86 98.3 0.457 2.9 4.2 2558
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) 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 PDB Entry 1IRD 1.8 16.37 2 2 26805 26803 1347 99.55 0.237 0.208 0.206 0.2067 0.237 0.2381 RANDOM 28.993
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] -0.05 -0.05 0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.389 r_dihedral_angle_3_deg 14.986 r_dihedral_angle_4_deg 12.709 r_dihedral_angle_1_deg 5.193 r_scangle_it 3.477 r_scbond_it 2.384 r_mcangle_it 1.551 r_angle_refined_deg 1.522 r_mcbond_it 1.011 r_symmetry_vdw_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.389 r_dihedral_angle_3_deg 14.986 r_dihedral_angle_4_deg 12.709 r_dihedral_angle_1_deg 5.193 r_scangle_it 3.477 r_scbond_it 2.384 r_mcangle_it 1.551 r_angle_refined_deg 1.522 r_mcbond_it 1.011 r_symmetry_vdw_refined 0.306 r_nbtor_refined 0.299 r_nbd_refined 0.218 r_xyhbond_nbd_refined 0.157 r_symmetry_hbond_refined 0.121 r_chiral_restr 0.113 r_metal_ion_refined 0.035 r_bond_refined_d 0.017 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2217 Nucleic Acid Atoms Solvent Atoms 152 Heterogen Atoms 99
Software Software Software Name Purpose d*TREK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection d*TREK data reduction