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Structure of an uncharacterized domain in polyribonucleotide nucleotidyltransferase from Streptococcus mutans UA159
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 297 0.1M Na Cacodylate pH6.5,0.2M Ca Acetate, 40% PEG 3000, VAPOR DIFFUSION, SITTING DROP, temperature 297K
Crystal Properties Matthews coefficient Solvent content 2.17 43.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.312 α = 90 b = 59.312 β = 90 c = 93.09 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 CCD ADSC QUANTUM 315r 2009-03-01 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97945,0.97931 APS 19-ID
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 1.7 50 99.8 0.082 65.5 22.7 11267 11267 -3 28.2
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 1.7 1.73 100 0.671 22.4 541
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 MAD THROUGHOUT 1.8 44.99 9492 9492 460 99.78 0.201 0.201 0.199 0.2095 0.236 0.2391 RANDOM 25.85
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] 1.36 0.68 1.36 -2.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.158 r_dihedral_angle_4_deg 25.032 r_dihedral_angle_3_deg 12.808 r_scangle_it 5.846 r_dihedral_angle_1_deg 4.515 r_scbond_it 3.357 r_mcangle_it 1.822 r_angle_refined_deg 1.538 r_angle_other_deg 0.956 r_mcbond_it 0.869
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.158 r_dihedral_angle_4_deg 25.032 r_dihedral_angle_3_deg 12.808 r_scangle_it 5.846 r_dihedral_angle_1_deg 4.515 r_scbond_it 3.357 r_mcangle_it 1.822 r_angle_refined_deg 1.538 r_angle_other_deg 0.956 r_mcbond_it 0.869 r_mcbond_other 0.258 r_chiral_restr 0.091 r_bond_refined_d 0.019 r_gen_planes_refined 0.007 r_bond_other_d 0.004 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 633 Nucleic Acid Atoms Solvent Atoms 90 Heterogen Atoms 5
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MLPHARE phasing DM phasing REFMAC refinement PDB_EXTRACT data extraction SBC-Collect data collection HKL-3000 data reduction HKL-3000 data scaling HKL-3000 phasing SHELXD phasing SHELXE model building SOLVE phasing RESOLVE phasing ARP/wARP model building CCP4 phasing O model building Coot model building