☰ Navigation Tabs
Crystal structure of a nucleoside triphosphate diphosphohydrolase (NTPDase) from the legume Trifolium repens in complex with adenine and phosphate
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 8 291 0.2 M ammonium dihydrogen orthophosphate, 15% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.18 43.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.91 α = 90 b = 52.811 β = 94.96 c = 72.18 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 ADSC QUANTUM 315r 2009-05-01 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 1.76 71.98 98.5 0.136 8.7 4.4 44133 17.27
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 1.76 53.71 35652 1887 93.17 0.18309 0.18092 0.1896 0.22411 0.2314 RANDOM 20.321
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 35.146 r_dihedral_angle_4_deg 18.98 r_dihedral_angle_3_deg 14.355 r_dihedral_angle_1_deg 6.712 r_long_range_B_refined 5.865 r_long_range_B_other 5.865 r_scangle_other 3.825 r_mcangle_it 2.626 r_mcangle_other 2.625 r_scbond_it 2.595
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.146 r_dihedral_angle_4_deg 18.98 r_dihedral_angle_3_deg 14.355 r_dihedral_angle_1_deg 6.712 r_long_range_B_refined 5.865 r_long_range_B_other 5.865 r_scangle_other 3.825 r_mcangle_it 2.626 r_mcangle_other 2.625 r_scbond_it 2.595 r_scbond_other 2.547 r_angle_refined_deg 2.046 r_mcbond_it 1.79 r_mcbond_other 1.782 r_angle_other_deg 0.931 r_chiral_restr 0.124 r_bond_refined_d 0.02 r_gen_planes_refined 0.01 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 3096 Nucleic Acid Atoms Solvent Atoms 393 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing