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Crystal structure of the D52N variant of cytosolic 5'-nucleotidase II in complex with deoxyguanosine monophosphate and deoxyadenosine triphosphate
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 = 91.55 α = 90 b = 127.43 β = 90 c = 130.5 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 99.5 0.07 19 5.6 34123 -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 99.5 0.4 4.26 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 2.3 48.68 32398 1724 99.55 0.17741 0.17502 0.1756 0.2218 0.2214 RANDOM 41.117
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] 0.74 0.04 -0.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.805 r_dihedral_angle_4_deg 19.81 r_dihedral_angle_3_deg 16.306 r_dihedral_angle_1_deg 6.233 r_scangle_it 3.32 r_scbond_it 2.295 r_angle_refined_deg 1.694 r_mcangle_it 1.309 r_mcbond_it 0.827 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.805 r_dihedral_angle_4_deg 19.81 r_dihedral_angle_3_deg 16.306 r_dihedral_angle_1_deg 6.233 r_scangle_it 3.32 r_scbond_it 2.295 r_angle_refined_deg 1.694 r_mcangle_it 1.309 r_mcbond_it 0.827 r_nbtor_refined 0.307 r_symmetry_vdw_refined 0.272 r_nbd_refined 0.202 r_xyhbond_nbd_refined 0.161 r_symmetry_hbond_refined 0.13 r_chiral_restr 0.108 r_metal_ion_refined 0.087 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_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 3784 Nucleic Acid Atoms Solvent Atoms 263 Heterogen Atoms 73
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing