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Crystal structure of human cytosolic 5'-nucleotidase III in complex with phosphate and magnesium
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 AND 20% GLYCEROL
Crystal Properties Matthews coefficient Solvent content 2.6 53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.459 α = 90 b = 101.036 β = 90 c = 77.046 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 CCD ADSC CCD 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 3 77.15 100 0.11 24.1 12.4 7057
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 3 3.16 100 0.42 6.3 13
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 3.01 50.19 6706 335 99.7 0.185 0.181 0.1739 0.268 0.2463 RANDOM 44.26
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] -0.06 0.23 -0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.732 r_dihedral_angle_4_deg 20.697 r_dihedral_angle_3_deg 19.569 r_dihedral_angle_1_deg 5.929 r_scangle_it 2.17 r_angle_refined_deg 1.361 r_scbond_it 1.29 r_mcangle_it 0.797 r_mcbond_it 0.448 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.732 r_dihedral_angle_4_deg 20.697 r_dihedral_angle_3_deg 19.569 r_dihedral_angle_1_deg 5.929 r_scangle_it 2.17 r_angle_refined_deg 1.361 r_scbond_it 1.29 r_mcangle_it 0.797 r_mcbond_it 0.448 r_nbtor_refined 0.31 r_nbd_refined 0.222 r_symmetry_vdw_refined 0.19 r_symmetry_hbond_refined 0.146 r_xyhbond_nbd_refined 0.129 r_chiral_restr 0.088 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 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 2190 Nucleic Acid Atoms Solvent Atoms 15 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing