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crystal structure of aspartate semialdehyde dehydrogenase II complexed with ASA from vibrio cholerae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YS4 PDB entry 1YS4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293 0.1M sodium citrate pH 5.5, 27% PEG8000, 0.3M ammonium acetate, 5mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.6 52.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.376 α = 90 b = 84.679 β = 102.07 c = 114.976 γ = 90
Symmetry Space Group C 1 2 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 4 2005-09-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-C 0.9 APS 14-BM-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 40 99.7 0.053 27 3.6 73968 70525
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2 96.1 0.33 5 4
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1YS4 2.03 40 70525 3747 99.42 0.19319 0.19112 0.23237 0.2183 RANDOM 30.037
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] 1.15 0.41 -0.11 -0.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.6 r_dihedral_angle_4_deg 18.263 r_dihedral_angle_3_deg 14.8 r_dihedral_angle_1_deg 5.942 r_scangle_it 2.53 r_scbond_it 1.616 r_angle_refined_deg 1.187 r_mcangle_it 1.152 r_mcbond_it 0.691 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.6 r_dihedral_angle_4_deg 18.263 r_dihedral_angle_3_deg 14.8 r_dihedral_angle_1_deg 5.942 r_scangle_it 2.53 r_scbond_it 1.616 r_angle_refined_deg 1.187 r_mcangle_it 1.152 r_mcbond_it 0.691 r_nbtor_refined 0.304 r_nbd_refined 0.205 r_symmetry_vdw_refined 0.173 r_xyhbond_nbd_refined 0.154 r_symmetry_hbond_refined 0.146 r_chiral_restr 0.086 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 7383 Nucleic Acid Atoms Solvent Atoms 600 Heterogen Atoms 9
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection DENZO data reduction SCALEPACK data scaling MOLREP phasing