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Crystal structure of O-ureido-L-serine synthase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Q3D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 298 Tris-HCl, polyethylene glycol 8,000, KH2PO4, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.32 46.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.48 α = 90 b = 154.13 β = 90.48 c = 118.52 γ = 90
Symmetry Space Group P 1 21 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 RAYONIX MX-225 2010-12-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0 SPring-8 BL41XU
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 2.25 100 99.9 0.09 9.1 3.8 122927 122927 25.3
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 2.25 2.37 100 0.475 2.8 3.8 17914
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 2Q3D 2.25 29.83 2 122865 122865 6178 99.7 0.209 0.209 0.2092 0.264 0.2638 RANDOM 51.4
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] 6.12 19.34 -0.32 -5.8
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 26.3 c_scangle_it 3.51 c_mcangle_it 2.95 c_scbond_it 2.54 c_mcbond_it 1.88 c_angle_deg 1.2 c_improper_angle_d 0.63 c_bond_d 0.006 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 26.3 c_scangle_it 3.51 c_mcangle_it 2.95 c_scbond_it 2.54 c_mcbond_it 1.88 c_angle_deg 1.2 c_improper_angle_d 0.63 c_bond_d 0.006 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 19095 Nucleic Acid Atoms Solvent Atoms 809 Heterogen Atoms 120
Software Software Software Name Purpose BSS data collection MOLREP phasing CNS refinement MOSFLM data reduction SCALA data scaling