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Crystal structure of C-termianl domain of N-acetylglutamate synthase from Vibrio parahaemolyticus
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 289 1.0 M Ammonium sulfate, 0.1 M Bis-Tris pH 5.5, 1% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 3.36 63.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.232 α = 90 b = 64.232 β = 90 c = 112.718 γ = 90
Symmetry Space Group P 41 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 315 2008-04-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97921 APS 19-ID
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 2.52 50 98.3 0.086 0.317 2.43 9.3 8509 8366 -3 67.7
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 2.52 2.54 100 0.87 2.43 9.7 197
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) 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 Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 2.52 50 8351 8351 389 98.62 0.21684 0.21684 0.21512 0.2173 0.25447 RANDOM 45.146
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] 0.83 0.83 -1.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.382 r_dihedral_angle_3_deg 17.776 r_dihedral_angle_4_deg 15.55 r_dihedral_angle_1_deg 5.948 r_scangle_it 2.091 r_scbond_it 1.425 r_angle_refined_deg 1.413 r_mcangle_it 1.11 r_mcbond_it 0.64 r_nbtor_refined 0.313
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.382 r_dihedral_angle_3_deg 17.776 r_dihedral_angle_4_deg 15.55 r_dihedral_angle_1_deg 5.948 r_scangle_it 2.091 r_scbond_it 1.425 r_angle_refined_deg 1.413 r_mcangle_it 1.11 r_mcbond_it 0.64 r_nbtor_refined 0.313 r_nbd_refined 0.222 r_symmetry_vdw_refined 0.218 r_symmetry_hbond_refined 0.183 r_xyhbond_nbd_refined 0.166 r_chiral_restr 0.096 r_bond_refined_d 0.013 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 1164 Nucleic Acid Atoms Solvent Atoms 51 Heterogen Atoms 13
Software Software Software Name Purpose REFMAC refinement SBC-Collect data collection HKL-3000 data reduction HKL-3000 data scaling HKL-3000 phasing