☰ Navigation Tabs
Crystal Structure of Deoxygenated Hemoglobin in Complex with an Allosteric Effector and Nitric Oxide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DN2 PDB entry 2DN2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIQUID DIFFUSION 6.5 295 0.2 M sodium acetate trihydrate, 0.1 M sodium cacodylate trihydrate, pH 6.5, 30% w/v PEG8000, anaerobic conditions
Crystal Properties Matthews coefficient Solvent content 2.49 50.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.878 α = 90 b = 98.419 β = 90 c = 65.444 γ = 90
Symmetry Space Group P 21 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++ 2013-04-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE Cu FINE FOCUS 1.54
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 1.85 29.54 98.2 0.084 12.3 5.53 53613 52628
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 1.85 1.92 94.3 0.313 4.5 4
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 PDB entry 2DN2 1.85 29.54 52628 2669 98.1 0.205 0.198 0.1943 0.253 0.2494 RANDOM 25.9
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] 0.98 2.26 -3.24
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 18.3 c_angle_deg 1.4 c_improper_angle_d 1.2 c_bond_d 0.01 c_mcbond_it c_mcangle_it c_scbond_it c_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4370 Nucleic Acid Atoms Solvent Atoms 973 Heterogen Atoms 270
Software Software Software Name Purpose d*TREK data scaling CNS refinement PDB_EXTRACT data extraction d*TREK data reduction PHENIX phasing