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Crystal structure of a nucleoside triphosphate diphosphohydrolase (NTPDase) from the legume Trifolium repens
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3CJI
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 2.24 45.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.996 α = 90 b = 53.592 β = 94.95 c = 72.835 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 IMAGE PLATE MAR scanner 345 mm plate 2009-11-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.54179
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 1.89 72.6 99 0.076 25.8 10.9 33604 21.2
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 3cji 1.89 24.54 30251 1633 95.37 0.18177 0.1789 0.186 0.23541 0.2373 RANDOM 23.147
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 0.03 -0.03 0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.946 r_dihedral_angle_4_deg 24.293 r_dihedral_angle_3_deg 15.23 r_long_range_B_refined 6.417 r_dihedral_angle_1_deg 6.407 r_long_range_B_other 6.268 r_scangle_other 3.824 r_mcangle_it 3.078 r_mcangle_other 3.078 r_scbond_it 2.583
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.946 r_dihedral_angle_4_deg 24.293 r_dihedral_angle_3_deg 15.23 r_long_range_B_refined 6.417 r_dihedral_angle_1_deg 6.407 r_long_range_B_other 6.268 r_scangle_other 3.824 r_mcangle_it 3.078 r_mcangle_other 3.078 r_scbond_it 2.583 r_scbond_other 2.557 r_mcbond_it 2.091 r_mcbond_other 2.09 r_angle_refined_deg 2.033 r_angle_other_deg 0.941 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 3071 Nucleic Acid Atoms Solvent Atoms 395 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing