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Crystal structure of Human Cytosolic 5'-Nucleotidase II (NT5C2, cN-II)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BDE PDB ENTRY 2BDE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 1.8 M MG2SO4 0.1 M TRIS PH 8.5
Crystal Properties Matthews coefficient Solvent content 3.17 61.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.465 α = 90 b = 128.034 β = 90 c = 130.415 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 MIRROR 2006-04-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 ESRF ID29
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 2.2 91.29 100 0.06 22.5 6 39212 23.5
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 2.2 2.32 100 0.15 11.5 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 2BDE 2.2 40 37234 1967 100 0.154 0.152 0.169 0.184 0.1939 RANDOM 7.85
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] -0.25 -0.04 0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.779 r_dihedral_angle_4_deg 18.438 r_dihedral_angle_3_deg 14.102 r_dihedral_angle_1_deg 5.958 r_scangle_it 3.171 r_scbond_it 2.105 r_angle_refined_deg 1.428 r_mcangle_it 1.206 r_mcbond_it 0.772 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.779 r_dihedral_angle_4_deg 18.438 r_dihedral_angle_3_deg 14.102 r_dihedral_angle_1_deg 5.958 r_scangle_it 3.171 r_scbond_it 2.105 r_angle_refined_deg 1.428 r_mcangle_it 1.206 r_mcbond_it 0.772 r_nbtor_refined 0.303 r_nbd_refined 0.193 r_symmetry_vdw_refined 0.192 r_symmetry_hbond_refined 0.173 r_xyhbond_nbd_refined 0.139 r_chiral_restr 0.101 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 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 3828 Nucleic Acid Atoms Solvent Atoms 445 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing