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Crystal structure of the unliganded (T-state) aspartate transcarbamoylase of the psychrophilic bacterium Moritella profunda
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6AT1 PDB Entry: 6AT1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 277 10 mg/ml, 0.1 M Tris, 1.5 M ammonium sulfate
, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.13 60.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 129.238 α = 90 b = 129.238 β = 90 c = 207.232 γ = 120
Symmetry Space Group P 32 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 MARRESEARCH 2004-07-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7A 0.92 EMBL/DESY, HAMBURG BW7A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.85 50 96.1 45685 45685
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.85 2.93 97.3
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 (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 MOLECULAR REPLACEMENT THROUGHOUT PDB Entry: 6AT1 2.85 20 43128 43128 2304 96.13 0.21392 0.21392 0.21164 0.2601 0.257 0.2467 RANDOM 51.473
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] -0.85 -0.42 -0.85 1.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.484 r_dihedral_angle_4_deg 20.439 r_dihedral_angle_3_deg 19.371 r_dihedral_angle_1_deg 6.511 r_scangle_it 1.688 r_angle_refined_deg 1.331 r_scbond_it 1.093 r_angle_other_deg 0.832 r_mcangle_it 0.761 r_mcbond_it 0.486
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.484 r_dihedral_angle_4_deg 20.439 r_dihedral_angle_3_deg 19.371 r_dihedral_angle_1_deg 6.511 r_scangle_it 1.688 r_angle_refined_deg 1.331 r_scbond_it 1.093 r_angle_other_deg 0.832 r_mcangle_it 0.761 r_mcbond_it 0.486 r_nbd_refined 0.212 r_symmetry_vdw_other 0.207 r_nbd_other 0.197 r_nbtor_refined 0.181 r_symmetry_vdw_refined 0.176 r_xyhbond_nbd_refined 0.155 r_symmetry_hbond_refined 0.155 r_nbtor_other 0.088 r_chiral_restr 0.076 r_mcbond_other 0.055 r_xyhbond_nbd_other 0.045 r_bond_refined_d 0.011 r_bond_other_d 0.006 r_gen_planes_refined 0.004 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9905 Nucleic Acid Atoms Solvent Atoms 36 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling PHASER phasing