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The crystal structure of the C-terminal beta-barrel of HpuA from Neisseria gonorrhoeae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5EC6 5EC6 residues 168-322
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.9 291 100 mM Hepes, 1.6 M ammonium sulfate, 0.8 % Peg 400, 200 mM sodium thiocyanate
Crystal Properties Matthews coefficient Solvent content 2.03 39.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.92 α = 90 b = 61.92 β = 90 c = 92.241 γ = 120
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 PILATUS3 6M 2014-03-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97949 Diamond I04
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 1.95 46.36 99.8 0.084 0.096 0.047 9.1 4 9586 9586
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 1.95 2.06 99.9 0.54 0.54 0.314 2.3 3.9 1392
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 residues 168-322 1.95 46.36 9078 506 99.77 0.1808 0.1781 0.1857 0.2303 0.2381 RANDOM 39.259
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] 0.91 0.45 0.91 -2.95
RMS Deviations Key Refinement Restraint Deviation r_mcangle_it 3.554 r_mcbond_it 2.541 r_mcbond_other 2.527 r_angle_refined_deg 1.384 r_angle_other_deg 0.722 r_chiral_restr 0.08 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 916 Nucleic Acid Atoms Solvent Atoms 58 Heterogen Atoms
Software Software Software Name Purpose SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction