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2.2A resolution structure of Holo hemophore HasA from Yersinia pestis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4JER PDB entry 4JER
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8.8 293 20% (w/v) PEG 3350, 50 mM Ches, 200 mM magnesium formate dihydrate, pH 8.8, vapor diffusion, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.64 53.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 139.369 α = 90 b = 69.559 β = 100.12 c = 232.317 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 PIXEL DECTRIS PILATUS 6M 2011-10-16 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.0000 APS 17-ID
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 2.2 228.701 98.2 0.087 3.5 109337 109337 -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) 1 2.2 2.24 97.7 0.668 2 3.6 5397
Refinement Statistics Diffraction ID Structure Solution 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB entry 4JER 2.2 38.624 1.84 109316 5497 97.94 0.1686 0.1658 0.1766 0.2231 0.2283 RANDOM 31.7917
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 15.869 f_angle_d 1.158 f_chiral_restr 0.081 f_bond_d 0.012 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13624 Nucleic Acid Atoms Solvent Atoms 720 Heterogen Atoms 440
Software Software Software Name Purpose SCALA data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction JDirector data collection XDS data reduction