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Crystal structure of the D52N variant of cytosolic 5'-nucleotidase II in complex with guanosine monophosphate and diadenosine tetraphosphate
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 PH 9.0, 10% PEG6000
Crystal Properties Matthews coefficient Solvent content 3.16 61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.54 α = 90 b = 127.36 β = 90 c = 130.24 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 20 99.9 0.08 17.37 5.6 51649 -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 2.2 100 0.44 4.1 5.6
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 45.79 49042 2605 99.94 0.17801 0.1758 0.177 0.21893 0.2183 RANDOM 33.892
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] 0.8 -0.62 -0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.482 r_dihedral_angle_4_deg 17.367 r_dihedral_angle_3_deg 15.132 r_dihedral_angle_1_deg 6.045 r_scangle_it 3.317 r_scbond_it 2.275 r_angle_refined_deg 1.588 r_mcangle_it 1.341 r_mcbond_it 0.861 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.482 r_dihedral_angle_4_deg 17.367 r_dihedral_angle_3_deg 15.132 r_dihedral_angle_1_deg 6.045 r_scangle_it 3.317 r_scbond_it 2.275 r_angle_refined_deg 1.588 r_mcangle_it 1.341 r_mcbond_it 0.861 r_nbtor_refined 0.305 r_symmetry_vdw_refined 0.227 r_symmetry_hbond_refined 0.218 r_nbd_refined 0.203 r_xyhbond_nbd_refined 0.167 r_chiral_restr 0.104 r_metal_ion_refined 0.073 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_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 3776 Nucleic Acid Atoms Solvent Atoms 394 Heterogen Atoms 126
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing