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Crystal structure of aminotransferase AspB (NP_207418.1) from HELICOBACTER PYLORI 26695 at 2.19 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277 15.0000% Glycerol, 8.5000% iso-Propanol, 17.0000% PEG-4000, 0.1M HEPES pH 7.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.28 45.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.648 α = 90 b = 106.249 β = 90 c = 80.201 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 2008-08-11 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.91162,0.97932 SSRL BL9-2
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 2.19 44.281 98.3 0.112 12.8 5.3 40833 -3 29.514
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 2.19 2.27 85.8 0.612 2.29
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 (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 2.19 44.281 40803 2056 98.46 0.161 0.159 0.1704 0.215 0.2197 RANDOM 43.55
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] 0.63 0.13 -0.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.376 r_dihedral_angle_4_deg 12.211 r_dihedral_angle_3_deg 10.377 r_scangle_it 5.549 r_scbond_it 4.291 r_dihedral_angle_1_deg 3.445 r_mcangle_it 2.274 r_angle_refined_deg 1.519 r_mcbond_it 1.498 r_angle_other_deg 1.012
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.376 r_dihedral_angle_4_deg 12.211 r_dihedral_angle_3_deg 10.377 r_scangle_it 5.549 r_scbond_it 4.291 r_dihedral_angle_1_deg 3.445 r_mcangle_it 2.274 r_angle_refined_deg 1.519 r_mcbond_it 1.498 r_angle_other_deg 1.012 r_mcbond_other 0.432 r_symmetry_vdw_other 0.239 r_nbd_refined 0.201 r_symmetry_hbond_refined 0.197 r_nbtor_refined 0.18 r_nbd_other 0.176 r_xyhbond_nbd_refined 0.174 r_symmetry_vdw_refined 0.138 r_chiral_restr 0.088 r_nbtor_other 0.086 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5988 Nucleic Acid Atoms Solvent Atoms 402 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction SHELXD phasing autoSHARP phasing