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Structure of Rattus norvegicus NTPDase2 in complex with calcium, AMP and phosphate
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 2.31 46.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.059 α = 90 b = 69.206 β = 90 c = 164.364 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 2007-05-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9184 BESSY 14.1
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 25.47 99.9 0.095 15.8 7 44443 2 21.8
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 99.7 0.457 2.7 4.9
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 25.47 43298 1074 99.86 0.16348 0.1624 0.1764 0.20557 0.2182 RANDOM 23.333
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] 0.33 0.19 -0.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.991 r_dihedral_angle_4_deg 13.372 r_dihedral_angle_3_deg 12.632 r_dihedral_angle_1_deg 5.737 r_scangle_it 4.692 r_scbond_it 3.052 r_mcangle_it 1.774 r_angle_refined_deg 1.619 r_mcbond_it 1.274 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.991 r_dihedral_angle_4_deg 13.372 r_dihedral_angle_3_deg 12.632 r_dihedral_angle_1_deg 5.737 r_scangle_it 4.692 r_scbond_it 3.052 r_mcangle_it 1.774 r_angle_refined_deg 1.619 r_mcbond_it 1.274 r_nbtor_refined 0.306 r_nbd_refined 0.208 r_xyhbond_nbd_refined 0.149 r_symmetry_vdw_refined 0.148 r_chiral_restr 0.119 r_symmetry_hbond_refined 0.119 r_metal_ion_refined 0.094 r_bond_refined_d 0.019 r_gen_planes_refined 0.008 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_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 3305 Nucleic Acid Atoms Solvent Atoms 387 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling SHARP phasing