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Crystal structure of human cytosolic 5'-nucleotidase III (cN-III, NT5C3) in complex with beryllium trifluoride
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2CN1 PDB ENTRY 2CN1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 24% PEG1500, 20% GLYCEROL
Crystal Properties Matthews coefficient Solvent content 2.6 52.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.265 α = 90 b = 99.388 β = 90 c = 78.041 γ = 90
Symmetry Space Group C 2 2 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 2006-02-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
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 2.5 78.09 99.7 0.09 15 5.9 12172 -3
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 2.5 2.64 100 0.42 2.8 6.2
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 PDB ENTRY 2CN1 2.5 30 11573 570 99.5 0.211 0.21 0.2093 0.242 0.2376 RANDOM 46.09
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] -1.22 1.61 -0.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.976 r_dihedral_angle_4_deg 21.309 r_dihedral_angle_3_deg 13.99 r_dihedral_angle_1_deg 5.407 r_scangle_it 1.292 r_angle_refined_deg 1.039 r_scbond_it 0.869 r_angle_other_deg 0.82 r_mcangle_it 0.466 r_mcbond_it 0.399
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.976 r_dihedral_angle_4_deg 21.309 r_dihedral_angle_3_deg 13.99 r_dihedral_angle_1_deg 5.407 r_scangle_it 1.292 r_angle_refined_deg 1.039 r_scbond_it 0.869 r_angle_other_deg 0.82 r_mcangle_it 0.466 r_mcbond_it 0.399 r_xyhbond_nbd_refined 0.39 r_symmetry_vdw_other 0.246 r_nbd_refined 0.204 r_symmetry_vdw_refined 0.183 r_nbtor_refined 0.173 r_nbd_other 0.167 r_symmetry_hbond_refined 0.096 r_nbtor_other 0.08 r_chiral_restr 0.057 r_bond_refined_d 0.009 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2188 Nucleic Acid Atoms Solvent Atoms 36 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing