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Staphylococcus aureus IsdB bound to human hemoglobin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DN1 2DN1, 3RTL, 4IJ2 experimental model PDB 3RTL 2DN1, 3RTL, 4IJ2 experimental model PDB 4IJ2 2DN1, 3RTL, 4IJ2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 298 0.1 M malonic acid pH 5.5, 2.2 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.99 58.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 140.815 α = 90 b = 209.114 β = 90 c = 70.431 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 CCD ADSC QUANTUM 315r 2014-05-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL7-1 1.000 SSRL BL7-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 3.6 50 99.8 0.116 0.127 0.051 6.6 6 46535 116.52
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.6 3.66 100 0.891 0.974 0.391 0.654 6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2DN1, 3RTL, 4IJ2 3.6 49.794 1.35 46499 3719 99.61 0.2556 0.2516 0.2602 0.3023 0.3024 111.2765
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 f_dihedral_angle_d 11.172 f_angle_d 0.679 f_chiral_restr 0.025 f_plane_restr 0.003 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11741 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 86
Software Software Software Name Purpose HKL-2000 data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction DENZO data reduction HKL data scaling