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The crystal structure of the Haemophilus influenzae HxuA secretion domain involved in the two-partner secretion pathway
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ODL PDB ENTRY 2ODL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 0.095M TRI SODIUM CITRATE pH 5.6, 5% GLYCEROL, 19% ISOPROPANOL, 12% PEG4000, 0.5M IMIDAZOLE pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.18 43.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.99 α = 90 b = 70.84 β = 98.1 c = 104.98 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 CCD ADSC QUANTUM 315r 2011-09-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.98011 SOLEIL PROXIMA 1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.5 41.9 89861 89775 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.59
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2ODL 1.5 41.9 2 89815 85287 4489 100 0.16154 0.159 0.21027 0.2023 RANDOM 20.866
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] 0.02 -0.08 0.01 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.003 r_dihedral_angle_4_deg 22.897 r_dihedral_angle_3_deg 13.643 r_scangle_it 9.217 r_dihedral_angle_1_deg 7.197 r_scbond_it 6.09 r_mcangle_it 4.246 r_rigid_bond_restr 3.186 r_mcbond_it 2.864 r_angle_refined_deg 2.236
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.003 r_dihedral_angle_4_deg 22.897 r_dihedral_angle_3_deg 13.643 r_scangle_it 9.217 r_dihedral_angle_1_deg 7.197 r_scbond_it 6.09 r_mcangle_it 4.246 r_rigid_bond_restr 3.186 r_mcbond_it 2.864 r_angle_refined_deg 2.236 r_chiral_restr 0.156 r_bond_refined_d 0.027 r_gen_planes_refined 0.013
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4278 Nucleic Acid Atoms Solvent Atoms 429 Heterogen Atoms
Software Software Software Name Purpose MOLREP phasing REFMAC refinement XDS data reduction XDS data scaling