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Crystal structure of the D52N variant of cytosolic 5'-nucleotidase II with a covalently modified Asn52
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2JC9 PDB ENTRY 2JC9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 0.1 M BICINE PH 9.0, 10% PEG 6000.
Crystal Properties Matthews coefficient Solvent content 3.19 61.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.095 α = 90 b = 128.222 β = 90 c = 130.439 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 MARMOSAIC 225 mm CCD 2007-11-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 ESRF ID23-2
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 2.1 50 96.4 0.11 11.7 5 43556
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 2.1 2.21 98.1 0.44 2.9 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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2JC9 2.1 65.23 41334 2224 96.04 0.18084 0.17845 0.2235 0.22517 RANDOM 25.414
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] 0.13 -0.04 -0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.111 r_dihedral_angle_3_deg 15.721 r_dihedral_angle_4_deg 12.763 r_dihedral_angle_1_deg 6.326 r_scangle_it 3.74 r_scbond_it 2.689 r_angle_refined_deg 1.625 r_mcangle_it 1.577 r_mcbond_it 1.012 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.111 r_dihedral_angle_3_deg 15.721 r_dihedral_angle_4_deg 12.763 r_dihedral_angle_1_deg 6.326 r_scangle_it 3.74 r_scbond_it 2.689 r_angle_refined_deg 1.625 r_mcangle_it 1.577 r_mcbond_it 1.012 r_nbtor_refined 0.307 r_nbd_refined 0.214 r_symmetry_vdw_refined 0.198 r_symmetry_hbond_refined 0.155 r_xyhbond_nbd_refined 0.142 r_chiral_restr 0.121 r_bond_refined_d 0.018 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 3764 Nucleic Acid Atoms Solvent Atoms 250 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing