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Crystal structure of Enterococcus faecalis putative nicotinate phosphoribosyltransferase, NEW YORK STRUCTURAL GENOMICS CONSORTIUM
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YTD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 290 100 mM HEPES, 2 M AMMONIUM SULFATE, 10% GLYCEROL, PH 7.50, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.47 49.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.325 α = 90 b = 110.627 β = 90 c = 154.189 γ = 90
Symmetry Space Group I 2 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 MIRRORS 2005-11-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 50 99.8 0.101 0.066 7.3 7 41720 41577 14.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.07 99.2 0.63 0.66 2.2 6.4 4095
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT 1YTD 2 20 41264 40207 1308 99.91 0.2213 0.17203 0.17066 0.1767 0.21362 0.1702 RANDOM 27.365
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] 0.07 1.63 -1.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.703 r_dihedral_angle_4_deg 24.085 r_dihedral_angle_3_deg 14.936 r_dihedral_angle_1_deg 8.12 r_scangle_it 1.868 r_mcangle_it 1.763 r_angle_refined_deg 1.365 r_scbond_it 1.207 r_mcbond_it 1.164 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.703 r_dihedral_angle_4_deg 24.085 r_dihedral_angle_3_deg 14.936 r_dihedral_angle_1_deg 8.12 r_scangle_it 1.868 r_mcangle_it 1.763 r_angle_refined_deg 1.365 r_scbond_it 1.207 r_mcbond_it 1.164 r_nbtor_refined 0.309 r_chiral_restr 0.226 r_symmetry_hbond_refined 0.223 r_xyhbond_nbd_refined 0.202 r_nbd_refined 0.185 r_symmetry_vdw_refined 0.158 r_bond_refined_d 0.012 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3884 Nucleic Acid Atoms Solvent Atoms 390 Heterogen Atoms 73
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement