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Structure of Rattus norvegicus NTPDase2 in complex with AMP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.2 277 100mM NaHEPES, 2% PEG 6000, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.29 46.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.07 α = 90 b = 68.903 β = 90 c = 163.83 γ = 90
Symmetry Space Group P 21 21 21
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 2007-03-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X12 0.979 EMBL/DESY, HAMBURG X12
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 1.8 29.63 98.5 0.087 15.9 7.2 43399 2 22
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) 1.8 1.9 90 0.436 2.4 4.8
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 SIRAS THROUGHOUT 1.8 29.63 42212 1120 98.22 0.1705 0.16958 0.1914 0.20568 0.2199 RANDOM 23.221
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] 0.61 0.35 -0.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.978 r_dihedral_angle_4_deg 13.353 r_dihedral_angle_3_deg 12.366 r_dihedral_angle_1_deg 5.668 r_scangle_it 3.912 r_scbond_it 2.529 r_angle_refined_deg 1.439 r_mcangle_it 1.431 r_mcbond_it 0.959 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.978 r_dihedral_angle_4_deg 13.353 r_dihedral_angle_3_deg 12.366 r_dihedral_angle_1_deg 5.668 r_scangle_it 3.912 r_scbond_it 2.529 r_angle_refined_deg 1.439 r_mcangle_it 1.431 r_mcbond_it 0.959 r_nbtor_refined 0.304 r_nbd_refined 0.202 r_symmetry_vdw_refined 0.165 r_symmetry_hbond_refined 0.15 r_xyhbond_nbd_refined 0.129 r_chiral_restr 0.097 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3286 Nucleic Acid Atoms Solvent Atoms 386 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling SHARP phasing