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Crystal Structure of Hemoglobin D from the Aldabra Giant Tortoise, Geochelone gigantea, at 1.65 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1V75 PDB ENTRY 1V75
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 293 50mM Tris-HCl, pH 7.5, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.96 58.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.244 α = 90 b = 62.138 β = 109.98 c = 53.926 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 100 IMAGE PLATE RIGAKU RAXIS VII 2003-12-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 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 1.65 40.48 94.7 0.031 7.39 39802 26.2
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) 1.65 1.71 90.6 0.211 5.8 7.14
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 1V75 1.65 40.48 39799 4000 94.6 0.193 0.1897 0.22 0.2153 RANDOM 28.7
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] -3.62 -0.13 8.26 -4.64
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 16.4 c_angle_deg 1.1 c_improper_angle_d 0.7 c_bond_d 0.005 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 16.4 c_angle_deg 1.1 c_improper_angle_d 0.7 c_bond_d 0.005 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 c_mcbond_it c_mcangle_it c_scbond_it c_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2292 Nucleic Acid Atoms Solvent Atoms 510 Heterogen Atoms 86
Software Software Software Name Purpose CNX refinement CrystalClear data reduction CrystalClear data scaling CNX phasing