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Crystal structure of the O-carbamoyltransferase TobZ M473I variant in complex with carbamoyl phosphate and ADP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3VEN PDB ENTRY 3VEN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 289 1.6 M sodium potassium tartrate, 0.1 M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 3.14 60.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.16 α = 90 b = 99.16 β = 90 c = 280.919 γ = 120
Symmetry Space Group P 61 2 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 IMAGE PLATE RIGAKU RAXIS IV++ 2011-08-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.5418
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 2.9 29.34 98.5 0.148 10.21 4.1 19007 18717 -3 16.45
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 2.9 3 98.6 0.421 3.82
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3VEN 2.9 29.336 1.36 19007 18708 934 98.58 0.1981 0.195 0.1873 0.2572 0.2471 INHERITED FROM 3VEN 17.541
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] 2.5183 2.5183 -5.0366
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.934 f_angle_d 1.269 f_chiral_restr 0.076 f_bond_d 0.009 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4378 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 37
Software Software Software Name Purpose XSCALE data scaling PHENIX refinement PDB_EXTRACT data extraction CrystalClear data collection XDS data reduction PHASER phasing