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Crystal structure of nicotinate phosphoribosyltransferase (target NYSGR-026035) from Vibrio cholerae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YIR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 25% PEG 3350, 0.2 M lithium sulfate, 0.1 M Tris HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.22 44.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.42 α = 90 b = 147.64 β = 90 c = 74.77 γ = 90
Symmetry Space Group P 21 21 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 PIXEL DECTRIS PILATUS 6M 2011-12-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.0 APS 17-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.8 50 99.9 0.046 86242 86142 -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 1.8 1.9 100
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 (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 1YIR 1.8 44.45 82138 78099 3896 95.08 0.16318 0.1613 0.1604 0.20056 0.2002 RANDOM 25.871
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.599 r_dihedral_angle_4_deg 19.72 r_dihedral_angle_3_deg 13.81 r_dihedral_angle_1_deg 6.13 r_angle_refined_deg 1.646 r_chiral_restr 0.121 r_bond_refined_d 0.019 r_gen_planes_refined 0.011 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.599 r_dihedral_angle_4_deg 19.72 r_dihedral_angle_3_deg 13.81 r_dihedral_angle_1_deg 6.13 r_angle_refined_deg 1.646 r_chiral_restr 0.121 r_bond_refined_d 0.019 r_gen_planes_refined 0.011 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_scbond_it r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6764 Nucleic Acid Atoms Solvent Atoms 751 Heterogen Atoms 15
Software Software Software Name Purpose JDirector data collection PHASER phasing REFMAC refinement XDS data reduction SCALA data scaling