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The crystal structure of HpuA from Kingella denitrificans in complex with human haemoglobin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5EC6 5EC6, 1HHO experimental model PDB 1HHO 5EC6, 1HHO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.8 277 100 mM Hepes, 18 % Peg 4,000, 10 % Isopropanol
Crystal Properties Matthews coefficient Solvent content 1.92 35.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.79 α = 90 b = 87.21 β = 98.13 c = 124.32 γ = 90
Symmetry Space Group P 1 21 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 2M 2014-10-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.3 123.071 96.9 0.175 0.191 0.075 8.6 6.5 49897 49897
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.42 97.8 0.818 0.818 0.353 2.1 6.3 7281
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 5EC6, 1HHO 2.3 123.07 47357 2491 96.65 0.2041 0.202 0.2069 0.2443 0.2493 RANDOM 33.173
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] 2.65 -0.13 0.11 -2.62
RMS Deviations Key Refinement Restraint Deviation r_mcangle_it 3.584 r_mcbond_it 2.316 r_mcbond_other 2.316 r_angle_refined_deg 1.504 r_angle_other_deg 1.04 r_chiral_restr 0.093 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_bond_other_d 0.005 r_gen_planes_other 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8742 Nucleic Acid Atoms Solvent Atoms 374 Heterogen Atoms 192
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction