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Crystal structure of the D52N variant of cytosolic 5'-nucleotidase II in complex with inosine monophosphate and 2,3-bisphosphoglycerate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2JCM PDB ENTRY 2JCM
Crystallization Crystal Properties Matthews coefficient Solvent content 3.16 61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.57 α = 90 b = 127.79 β = 90 c = 130.61 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 99.4 0.07 17.8 5.4 34216 -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 0.41 4.6 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-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 32486 1729 99.42 0.17893 0.17627 0.22868 0.2216 RANDOM 35.669
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] 1.16 1.08 -2.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.158 r_dihedral_angle_4_deg 20.439 r_dihedral_angle_3_deg 16.823 r_dihedral_angle_1_deg 6.592 r_scangle_it 4.41 r_scbond_it 3.059 r_mcangle_it 2.021 r_angle_refined_deg 1.849 r_mcbond_it 1.218 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.158 r_dihedral_angle_4_deg 20.439 r_dihedral_angle_3_deg 16.823 r_dihedral_angle_1_deg 6.592 r_scangle_it 4.41 r_scbond_it 3.059 r_mcangle_it 2.021 r_angle_refined_deg 1.849 r_mcbond_it 1.218 r_nbtor_refined 0.31 r_symmetry_vdw_refined 0.236 r_nbd_refined 0.209 r_symmetry_hbond_refined 0.168 r_xyhbond_nbd_refined 0.163 r_chiral_restr 0.126 r_metal_ion_refined 0.063 r_bond_refined_d 0.021 r_gen_planes_refined 0.009 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 3767 Nucleic Acid Atoms Solvent Atoms 258 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing