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Crystal structure of parrot hemoglobin (Psittacula krameri) at pH 7.5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1C40
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 291 10% PEG 3350, phosphate buffer pH 7.5, VAPOR DIFFUSION, temperature 291K
Crystal Properties Matthews coefficient Solvent content 3.02 59.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.676 α = 90 b = 64.268 β = 109.35 c = 56.396 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 291 IMAGE PLATE MAR scanner 345 mm plate 2007-12-20 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) 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 14.95 6543
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 3 14.95
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-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 1C40 3 14.39 6543 712 95.97 0.19822 0.18975 0.1902 0.27448 0.2738 RANDOM 28.867
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.898 r_dihedral_angle_3_deg 21.687 r_dihedral_angle_4_deg 21.35 r_dihedral_angle_1_deg 6.714 r_scangle_it 2.315 r_angle_refined_deg 1.689 r_scbond_it 1.411 r_mcangle_it 1.122 r_mcbond_it 0.617 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.898 r_dihedral_angle_3_deg 21.687 r_dihedral_angle_4_deg 21.35 r_dihedral_angle_1_deg 6.714 r_scangle_it 2.315 r_angle_refined_deg 1.689 r_scbond_it 1.411 r_mcangle_it 1.122 r_mcbond_it 0.617 r_nbtor_refined 0.31 r_nbd_refined 0.242 r_xyhbond_nbd_refined 0.18 r_symmetry_vdw_refined 0.169 r_symmetry_hbond_refined 0.138 r_chiral_restr 0.129 r_bond_refined_d 0.016 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2213 Nucleic Acid Atoms Solvent Atoms 15 Heterogen Atoms 86
Software Software Software Name Purpose REFMAC refinement MAR345 data collection AUTOMAR data reduction SCALEPACK data scaling AMoRE phasing