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Crystal structure of a nucleoside triphosphate diphosphohydrolase (NTPDase) from the legume Vigna unguiculata subsp. cylindrica (Dolichos biflorus) in complex with phosphate and manganese
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5U7P
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 291 0.2 M MgCl2, 50 mM acetate, pH 5.0, 9-12% MPD, 10-2-% PEG 3350, 5 mM AMP
Crystal Properties Matthews coefficient Solvent content 2.88 57.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.09 α = 90 b = 71.11 β = 139.45 c = 93.27 γ = 90
Symmetry Space Group C 1 2 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 ADSC QUANTUM 315r 2011-06-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.9537 Australian Synchrotron MX2
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 2.6 46.62 100 0.099 15.9 7.5 15843 30.59
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 5u7p 2.6 46.62 15045 789 99.92 0.17191 0.16796 0.1783 0.24804 0.2539 RANDOM 31.664
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
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.939 r_dihedral_angle_3_deg 18.388 r_dihedral_angle_4_deg 18.289 r_dihedral_angle_1_deg 7.356 r_long_range_B_refined 5.724 r_long_range_B_other 5.668 r_scangle_other 4.018 r_mcangle_it 3.019 r_mcangle_other 3.018 r_scbond_it 2.528
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.939 r_dihedral_angle_3_deg 18.388 r_dihedral_angle_4_deg 18.289 r_dihedral_angle_1_deg 7.356 r_long_range_B_refined 5.724 r_long_range_B_other 5.668 r_scangle_other 4.018 r_mcangle_it 3.019 r_mcangle_other 3.018 r_scbond_it 2.528 r_scbond_other 2.525 r_mcbond_it 1.925 r_mcbond_other 1.923 r_angle_refined_deg 1.89 r_angle_other_deg 0.903 r_chiral_restr 0.099 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3147 Nucleic Acid Atoms Solvent Atoms 137 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHENIX phasing