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Crystal structure of the apoform of the D52N variant of cytosolic 5'- nucleotidase II
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2JCM PDB ENTRY 2JCM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 0.1 M BICINE PH9.0, 10% PEG6000
Crystal Properties Matthews coefficient Solvent content 3.16 61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.12 α = 90 b = 126.51 β = 90 c = 130.08 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 PIXEL DECTRIS PILATUS 6M DYNAMICALLY BENDABLE 2008-01-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA SLS X06SA
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 2.3 20 99.9 0.07 17.37 5.5 34076 -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 2.3 2.4 100 0.6 3.6 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 2JCM 2.3 48.68 32347 1727 99.91 0.18476 0.18234 0.1802 0.22901 0.2284 RANDOM 44.2
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] -1.21 0.74 0.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.498 r_dihedral_angle_4_deg 18.137 r_dihedral_angle_3_deg 17.109 r_dihedral_angle_1_deg 6.631 r_scangle_it 3.183 r_scbond_it 2.192 r_angle_refined_deg 1.548 r_mcangle_it 1.326 r_mcbond_it 0.796 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.498 r_dihedral_angle_4_deg 18.137 r_dihedral_angle_3_deg 17.109 r_dihedral_angle_1_deg 6.631 r_scangle_it 3.183 r_scbond_it 2.192 r_angle_refined_deg 1.548 r_mcangle_it 1.326 r_mcbond_it 0.796 r_nbtor_refined 0.305 r_nbd_refined 0.197 r_symmetry_vdw_refined 0.195 r_symmetry_hbond_refined 0.187 r_xyhbond_nbd_refined 0.149 r_chiral_restr 0.106 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 3805 Nucleic Acid Atoms Solvent Atoms 236 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing