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Helicobacter pylori PseC, aminotransferase involved in the biosynthesis of pseudoaminic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MDO PDB ENTRY 1MDO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 293 mixing 1.5 microL of protein in buffer with 1.5 microL of reservoir solution containing 0.2 M ammonium acetate, 0.1 M trisodium citrate pH 5.6, 30% PEG 4000., VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.87 57.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.691 α = 90 b = 155.424 β = 90 c = 71.482 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 ADSC QUANTUM 4 2004-06-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X26C 1.1 NSLS X26C
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 2.483 77.62 98.9 0.075 40 4.7 35038 35038 1 1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 1MDO 2.483 77.62 34990 33236 1754 99.16 0.21043 0.20729 0.26931 0.258 RANDOM 51.902
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] -0.52 -0.71 1.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.985 r_dihedral_angle_3_deg 17.41 r_dihedral_angle_4_deg 16.979 r_dihedral_angle_1_deg 5.912 r_scangle_it 4.959 r_scbond_it 3.192 r_mcangle_it 2.933 r_mcbond_it 1.677 r_angle_refined_deg 1.264 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.985 r_dihedral_angle_3_deg 17.41 r_dihedral_angle_4_deg 16.979 r_dihedral_angle_1_deg 5.912 r_scangle_it 4.959 r_scbond_it 3.192 r_mcangle_it 2.933 r_mcbond_it 1.677 r_angle_refined_deg 1.264 r_nbtor_refined 0.306 r_nbd_refined 0.213 r_symmetry_vdw_refined 0.182 r_xyhbond_nbd_refined 0.12 r_chiral_restr 0.083 r_symmetry_hbond_refined 0.045 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5895 Nucleic Acid Atoms Solvent Atoms 119 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing