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Crystal structure determination of cat (Felis silvestris catus) hemoglobin at 2.0 angstrom resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3D4X PDB ENTRY 3D4X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 50% PEG 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.23 44.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.507 α = 90 b = 73.217 β = 103.38 c = 70.38 γ = 90
Symmetry Space Group P 1 21 1
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 MAR scanner 345 mm plate mirrors 2008-02-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.5417
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 2 30 93.8 0.0739 5.1 2.5 35212 33292 2.3 2.3
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) 2 2.07 92.2 0.3237 1.2 2.55 2785
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 (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 3D4X 2 29.72 2.3 2.3 35212 31437 3460 93.89 0.25317 0.24826 0.25 0.29806 0.2638 RANDOM 26.551
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] -0.6 0.12 -0.13 0.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.516 r_dihedral_angle_3_deg 17.118 r_dihedral_angle_4_deg 12.785 r_dihedral_angle_1_deg 5.834 r_scangle_it 2.393 r_scbond_it 1.763 r_angle_refined_deg 1.367 r_mcangle_it 1.017 r_mcbond_it 0.729 r_nbtor_refined 0.292
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.516 r_dihedral_angle_3_deg 17.118 r_dihedral_angle_4_deg 12.785 r_dihedral_angle_1_deg 5.834 r_scangle_it 2.393 r_scbond_it 1.763 r_angle_refined_deg 1.367 r_mcangle_it 1.017 r_mcbond_it 0.729 r_nbtor_refined 0.292 r_symmetry_vdw_refined 0.221 r_nbd_refined 0.215 r_symmetry_hbond_refined 0.202 r_xyhbond_nbd_refined 0.163 r_chiral_restr 0.092 r_bond_refined_d 0.013 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4404 Nucleic Acid Atoms Solvent Atoms 217 Heterogen Atoms 172
Software Software Software Name Purpose MAR345dtb data collection PHASER phasing REFMAC refinement AUTOMAR data reduction SCALEPACK data scaling