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Crystal structure of Human Cytosolic 5'-Nucleotidase II in complex with adenosine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2J2C PDB ENTRY 2J2C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 1.8 M MAGNESIUM SULFATE, 0.1 M TRIS PH 8.5
Crystal Properties Matthews coefficient Solvent content 3.16 61.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.273 α = 90 b = 127.983 β = 90 c = 130.601 γ = 90
Symmetry Space Group I 2 2 2
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 CCD MIRRORS 2006-10-08 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 1.5 74.95 100 0.08 17.6 6.4 122218
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 1.5 1.58 100 0.44 2.3 3.7
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 2J2C 1.5 74.33 115715 6117 100 0.162 0.16 0.1689 0.186 0.1924 RANDOM 16.18
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] 0.18 -0.17 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.804 r_dihedral_angle_4_deg 16.754 r_dihedral_angle_3_deg 12.78 r_dihedral_angle_1_deg 5.739 r_scangle_it 3.686 r_scbond_it 2.822 r_mcangle_it 1.871 r_mcbond_it 1.576 r_angle_refined_deg 1.405 r_angle_other_deg 0.887
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.804 r_dihedral_angle_4_deg 16.754 r_dihedral_angle_3_deg 12.78 r_dihedral_angle_1_deg 5.739 r_scangle_it 3.686 r_scbond_it 2.822 r_mcangle_it 1.871 r_mcbond_it 1.576 r_angle_refined_deg 1.405 r_angle_other_deg 0.887 r_symmetry_vdw_refined 0.441 r_symmetry_vdw_other 0.359 r_nbd_refined 0.217 r_nbd_other 0.19 r_nbtor_refined 0.188 r_xyhbond_nbd_refined 0.149 r_symmetry_hbond_refined 0.149 r_chiral_restr 0.089 r_nbtor_other 0.083 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 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 3808 Nucleic Acid Atoms Solvent Atoms 494 Heterogen Atoms 76
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing