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Human cytosolic 5'-nucleotidase II in complex with Anthraquinone-2,6- disulfonic acid
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 VAPOR DIFFUSION, HANGING DROP 8.5 277 magnesium sulphate and Tris buffer, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.89 57.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.11 α = 90 b = 126.83 β = 90 c = 130.4 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 QUANTUM 315r 2010-06-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A 0.979696 ESRF BM30A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.9 90.9 98.6 16880 16022 1 1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 2.9 48.92 1 16872 16022 858 98.6 0.188 0.184 0.1818 0.249 0.2406 RANDOM 32.302
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] 1.38 -0.6 -0.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.917 r_dihedral_angle_3_deg 19.458 r_dihedral_angle_4_deg 18.465 r_dihedral_angle_1_deg 6.353 r_scangle_it 3.56 r_scbond_it 2.042 r_angle_refined_deg 1.659 r_mcangle_it 1.247 r_mcbond_it 0.612 r_chiral_restr 0.114
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.917 r_dihedral_angle_3_deg 19.458 r_dihedral_angle_4_deg 18.465 r_dihedral_angle_1_deg 6.353 r_scangle_it 3.56 r_scbond_it 2.042 r_angle_refined_deg 1.659 r_mcangle_it 1.247 r_mcbond_it 0.612 r_chiral_restr 0.114 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3816 Nucleic Acid Atoms Solvent Atoms 58 Heterogen Atoms 56
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement XDS data reduction XSCALE data scaling