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Crystal structure of a putative nicotinate phosphoribosyltransferase (yor209c, npt1) from saccharomyces cerevisiae at 1.75 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION,SITTING DROP,NANODROP 277 0.06M MES, 0.04M MES_Na, 14% PEG MME 5000 , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K 2 VAPOR DIFFUSION,SITTING DROP,NANODROP 277 15% PEG MME 5000, 0.06M MES, 0.04M MES_Na , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.32 46.9 2.29 45.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.406 α = 97.35 b = 83.103 β = 95.67 c = 107.237 γ = 97.99
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 2004-01-08 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD ADSC 2003-12-19 M MAD 1,2 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.1 ALS 8.2.1 2 SYNCHROTRON ALS BEAMLINE 8.2.2 1.0332, 0.9798 ALS 8.2.2
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 1.75 50 96.81 0.075 18.09 3.79 177740 28.97
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 1.75 1.81 90.05 0.451 1.64 2.23 16630
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 (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 1.75 48.24 168817 8921 96.23 0.17163 0.16964 0.1812 0.20962 0.1838 RANDOM 7.224
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] -0.03 0.01 -0.03 0.04 0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.483 r_dihedral_angle_4_deg 17.756 r_dihedral_angle_3_deg 13.068 r_scangle_it 6.54 r_dihedral_angle_1_deg 6.168 r_scbond_it 4.736 r_mcangle_it 2.854 r_mcbond_it 2.16 r_angle_refined_deg 1.544 r_angle_other_deg 0.859
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.483 r_dihedral_angle_4_deg 17.756 r_dihedral_angle_3_deg 13.068 r_scangle_it 6.54 r_dihedral_angle_1_deg 6.168 r_scbond_it 4.736 r_mcangle_it 2.854 r_mcbond_it 2.16 r_angle_refined_deg 1.544 r_angle_other_deg 0.859 r_mcbond_other 0.558 r_symmetry_vdw_refined 0.238 r_symmetry_vdw_other 0.235 r_nbd_refined 0.215 r_nbtor_refined 0.182 r_nbd_other 0.176 r_symmetry_hbond_refined 0.168 r_xyhbond_nbd_refined 0.118 r_chiral_restr 0.094 r_nbtor_other 0.085 r_bond_refined_d 0.018 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13317 Nucleic Acid Atoms Solvent Atoms 1271 Heterogen Atoms 47
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling SHELXCD phasing SHARP phasing REFMAC refinement SHELXD phasing