☰ Navigation Tabs
Crystal structure of putative Xaa-His dipeptidase (YP_718209.1) from Haemophilus somnus 129PT at 2.11 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.9 277 NANODROP, 2.0M (NH4)2SO4, 5.0% Isopropanol, 0.1M Citrate pH 4.9, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 4.17 70.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 173.922 α = 90 b = 84.293 β = 90 c = 123.204 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 MARMOSAIC 325 mm CCD Flat collimating mirror, toroid focusing mirror 2007-06-03 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.97920, 0.91837, 0.97908 SSRL BL9-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.11 47.836 98.1 0.086 0.086 8.2 3.8 102365 30.01
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.11 2.22 99.4 0.584 0.584 1.3 3.8 15031
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 MAD THROUGHOUT 2.11 47.836 102314 5107 97.68 0.221 0.221 0.22 0.2253 0.244 0.2483 RANDOM 47.21
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] -2.02 3.6 -1.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.759 r_dihedral_angle_4_deg 17.546 r_dihedral_angle_3_deg 15.159 r_dihedral_angle_1_deg 6.414 r_scangle_it 3.932 r_scbond_it 2.803 r_mcangle_it 2.242 r_mcbond_it 1.446 r_angle_refined_deg 1.271 r_angle_other_deg 0.828
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.759 r_dihedral_angle_4_deg 17.546 r_dihedral_angle_3_deg 15.159 r_dihedral_angle_1_deg 6.414 r_scangle_it 3.932 r_scbond_it 2.803 r_mcangle_it 2.242 r_mcbond_it 1.446 r_angle_refined_deg 1.271 r_angle_other_deg 0.828 r_mcbond_other 0.375 r_nbd_refined 0.197 r_symmetry_vdw_refined 0.186 r_nbd_other 0.184 r_symmetry_hbond_refined 0.174 r_nbtor_refined 0.173 r_symmetry_vdw_other 0.164 r_xyhbond_nbd_refined 0.151 r_nbtor_other 0.085 r_chiral_restr 0.072 r_bond_refined_d 0.012 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7212 Nucleic Acid Atoms Solvent Atoms 466 Heterogen Atoms 208
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building SCALA data scaling PDB_EXTRACT data extraction MAR345 data collection XDS data reduction autoSHARP phasing