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Lactobacillus casei Y261M in complex with substrate, dUMP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 295 Vapor diffusion against 20 mM KPO4 from protein solutions in the same buffer with 15-20 mM ammonium sulfate, DTT, and 38mM dUMP, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.93 57.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.52 α = 90 b = 78.52 β = 90 c = 240.93 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 295 IMAGE PLATE RIGAKU RAXIS IIC 1996-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.54178
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 2.4 39.32 94.5 0.1 17124 17124 -3
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 2.4 2.55 87.2 3.4 2547
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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 2.4 39.32 17124 17124 1704 94.5 0.207 0.203 0.203 0.2006 0.276 0.275 RANDOM 35.6
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] -1.31 -0.64 -1.31 2.63
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 25.6 c_scangle_it 4.71 c_scbond_it 3.32 c_angle_deg 2.6 c_mcangle_it 2.51 c_improper_angle_d 2.14 c_mcbond_it 1.46 c_bond_d 0.029 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 25.6 c_scangle_it 4.71 c_scbond_it 3.32 c_angle_deg 2.6 c_mcangle_it 2.51 c_improper_angle_d 2.14 c_mcbond_it 1.46 c_bond_d 0.029 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 2589 Nucleic Acid Atoms Solvent Atoms 78 Heterogen Atoms 20
Software Software Software Name Purpose CNS refinement CCP4 data scaling CNS phasing