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Crystal structure of Human Cytosolic 5'-Nucleotidase II in complex with beryllium trifluoride
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 = 91.48 α = 90 b = 128.26 β = 90 c = 131.01 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 2.15 20 98 0.16 7.14 5.2 41406 -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 2.15 2.2 99.8 0.5 3.36 5.5
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 2.15 20.67 39316 2089 98.1 0.213 0.21 0.2173 0.266 0.2664 RANDOM 13.27
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] -0.45 -0.47 0.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.187 r_dihedral_angle_4_deg 16.755 r_dihedral_angle_3_deg 15.654 r_dihedral_angle_1_deg 6.557 r_scangle_it 3.526 r_scbond_it 2.385 r_angle_refined_deg 1.759 r_mcangle_it 1.449 r_mcbond_it 0.916 r_nbtor_refined 0.313
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.187 r_dihedral_angle_4_deg 16.755 r_dihedral_angle_3_deg 15.654 r_dihedral_angle_1_deg 6.557 r_scangle_it 3.526 r_scbond_it 2.385 r_angle_refined_deg 1.759 r_mcangle_it 1.449 r_mcbond_it 0.916 r_nbtor_refined 0.313 r_nbd_refined 0.21 r_symmetry_vdw_refined 0.199 r_xyhbond_nbd_refined 0.153 r_symmetry_hbond_refined 0.152 r_chiral_restr 0.117 r_bond_refined_d 0.019 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_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 3812 Nucleic Acid Atoms Solvent Atoms 260 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing