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Crystal structure of Idp01880, putative NTP pyrophosphohydrolase of Salmonella typhimurium LT2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GRN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 293 200nl of protein at 20mg/ml was mixed with 200nl of 0.1M Ammonium acetate, 0.1M Bis-Tris pH5.5, 17%w/v PEG10000 suspended over reservoir of 60 ul of 1.5M NaCl, vapor diffusion, sitting drop, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.09 41.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.498 α = 90 b = 66.268 β = 113.87 c = 50.836 γ = 90
Symmetry Space Group P 1 21 1
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 MARMOSAIC 225 mm CCD 2009-10-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 1.000 APS 22-BM
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 1.86 40 97.2 0.067 14.2 3.2 22053
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) 1.86 1.93 79.4 0.211 2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT 3GRN 1.86 38.06 20995 1041 96.99 0.17 0.16694 0.1752 0.23348 0.245 RANDOM 31.844
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] 0.18 1.11 0.18 0.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.907 r_dihedral_angle_4_deg 18.247 r_dihedral_angle_3_deg 14.475 r_dihedral_angle_1_deg 6.782 r_angle_refined_deg 1.552 r_angle_other_deg 1.196 r_chiral_restr 0.107 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 r_bond_other_d 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.907 r_dihedral_angle_4_deg 18.247 r_dihedral_angle_3_deg 14.475 r_dihedral_angle_1_deg 6.782 r_angle_refined_deg 1.552 r_angle_other_deg 1.196 r_chiral_restr 0.107 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 r_bond_other_d 0.004 r_gen_planes_other 0.004 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 2262 Nucleic Acid Atoms Solvent Atoms 204 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction SERGUI data collection HKL-2000 data reduction HKL-2000 data scaling BALBES phasing