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CRYSTAL STRUCTURE OF A PYRIMIDINE REDUCTASE-LIKE PROTEIN (DIP1392) FROM CORYNEBACTERIUM DIPHTHERIAE NCTC AT 2.30 A RESOLUTION
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 NANODROP, 0.2M Potassium nitrate, 20.0% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 277K 2 VAPOR DIFFUSION, SITTING DROP 6.9 277 NANODROP, 0.2M Potassium nitrate, 20.0% PEG 3350, No Buffer pH 6.9, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.51 α = 90 b = 113.51 β = 90 c = 55.94 γ = 120
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 2006-09-22 M SINGLE WAVELENGTH 2 2 x-ray 100 CCD MARMOSAIC 325 mm CCD Flat collimating mirror, toroid focusing mirror 2006-06-18 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.3 1.00000 ALS 5.0.3 2 SYNCHROTRON SSRL BEAMLINE BL9-2 0.97922, 0.97939, 0.91162 SSRL BL9-2
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 2.3 28.273 97.3 0.052 11.61 3.66 18260 46.09
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 2.3 2.38 92.9 0.41 1.76
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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 MAD THROUGHOUT 2.3 28.273 18113 922 98.39 0.175 0.175 0.173 0.1838 0.225 0.2315 RANDOM 60.7
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] 0.08 0.04 0.08 -0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.576 r_dihedral_angle_4_deg 18.875 r_dihedral_angle_3_deg 13.499 r_dihedral_angle_1_deg 7.053 r_scangle_it 6.955 r_scbond_it 5.366 r_mcangle_it 2.897 r_mcbond_it 1.742 r_angle_refined_deg 1.449 r_angle_other_deg 0.926
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.576 r_dihedral_angle_4_deg 18.875 r_dihedral_angle_3_deg 13.499 r_dihedral_angle_1_deg 7.053 r_scangle_it 6.955 r_scbond_it 5.366 r_mcangle_it 2.897 r_mcbond_it 1.742 r_angle_refined_deg 1.449 r_angle_other_deg 0.926 r_mcbond_other 0.362 r_symmetry_vdw_other 0.254 r_nbd_refined 0.217 r_nbd_other 0.204 r_nbtor_refined 0.174 r_symmetry_vdw_refined 0.167 r_xyhbond_nbd_refined 0.134 r_symmetry_hbond_refined 0.11 r_nbtor_other 0.088 r_chiral_restr 0.076 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1846 Nucleic Acid Atoms Solvent Atoms 113 Heterogen Atoms 64
Software Software Software Name Purpose MolProbity model building SOLVE phasing REFMAC refinement XSCALE data scaling PDB_EXTRACT data extraction ADSC data collection XDS data reduction