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X-ray structure of mouse pyrimidine 5'-nucleotidase type 1 with lead(II) bound in active site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BDU pdb entry 2BDU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 277 PROTEIN SOLUTION (10 MG/ML PROTEIN,
0.005 M BIS TRIS, 0.050 M SODIUM CHLORIDE, 0.003 M SODIUM
AZIDE, 0.0003 M TCEP, PH 6.0) MIXED IN A 1:1 RATIO WITH THE
WELL SOLUTION (20-25% PEG 8K, 0.10 M PIPES PH 6.5) CRYSTALS SOAKED
FOR 5 MINUTES IN WELL SOLUTION WITH 0.001 M Lead(II) Acetate, vapor diffusion, hanging drop, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3 58.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 134.549 α = 90 b = 134.549 β = 90 c = 39.226 γ = 120
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 BRUKER PROTEUM-R MONTEL OPTICS 2005-12-27 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.5418
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 2.35 67.27 100 0.0959 26.05 24.19 33118
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 2.35 2.4 100 0.5302 3.45 6.76 2063
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 (All) 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 2BDU 2.35 67.27 33098 1668 99.961 0.153 0.153 0.1494 0.1487 0.2293 0.228 RANDOM 38.913
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] 0.172 0.086 0.172 -0.257
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.22 r_dihedral_angle_4_deg 24.168 r_dihedral_angle_3_deg 16.393 r_dihedral_angle_1_deg 6.283 r_scangle_it 3.775 r_scbond_it 2.498 r_angle_refined_deg 1.507 r_mcangle_it 1.343 r_mcbond_it 0.765 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.22 r_dihedral_angle_4_deg 24.168 r_dihedral_angle_3_deg 16.393 r_dihedral_angle_1_deg 6.283 r_scangle_it 3.775 r_scbond_it 2.498 r_angle_refined_deg 1.507 r_mcangle_it 1.343 r_mcbond_it 0.765 r_nbtor_refined 0.306 r_symmetry_hbond_refined 0.276 r_symmetry_vdw_refined 0.209 r_nbd_refined 0.207 r_xyhbond_nbd_refined 0.196 r_chiral_restr 0.112 r_metal_ion_refined 0.104 r_bond_refined_d 0.017 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4652 Nucleic Acid Atoms Solvent Atoms 862 Heterogen Atoms 32
Software Software Software Name Purpose SAINT data scaling REFMAC refinement PDB_EXTRACT data extraction SAINT data reduction SADABS data scaling MOLREP phasing