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X-ray structure of mouse pyrimidine 5'-nucleotidase type 1, phospho-enzyme intermediate analog with Beryllium fluoride
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 20 MINUTES IN WELL SOLUTION WITH 0.060 M magnesium chloride,
0.003 M beryllium fluoride, 0.050 M sodium fluoride, vapor diffusion, hanging drop, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.98 58.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 134.834 α = 90 b = 134.834 β = 90 c = 38.945 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 2006-01-20 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 2.3 67.42 93.9 0.1278 11.32 7.7 33047
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 2.35 83.8 0.6356 1.99 4.11 1805
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 2.3 67.42 33027 1673 93.901 0.184 0.184 0.1799 0.1781 0.2585 0.2558 RANDOM 38.491
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] -0.155 -0.078 -0.155 0.233
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.608 r_dihedral_angle_4_deg 19.773 r_dihedral_angle_3_deg 16.423 r_dihedral_angle_1_deg 6.504 r_scangle_it 3.063 r_scbond_it 2.127 r_angle_refined_deg 1.664 r_mcangle_it 1.219 r_mcbond_it 0.84 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.608 r_dihedral_angle_4_deg 19.773 r_dihedral_angle_3_deg 16.423 r_dihedral_angle_1_deg 6.504 r_scangle_it 3.063 r_scbond_it 2.127 r_angle_refined_deg 1.664 r_mcangle_it 1.219 r_mcbond_it 0.84 r_nbtor_refined 0.305 r_nbd_refined 0.209 r_symmetry_vdw_refined 0.186 r_xyhbond_nbd_refined 0.18 r_symmetry_hbond_refined 0.174 r_chiral_restr 0.119 r_metal_ion_refined 0.051 r_bond_refined_d 0.018 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4660 Nucleic Acid Atoms Solvent Atoms 538 Heterogen Atoms 2
Software Software Software Name Purpose SAINT data scaling REFMAC refinement PDB_EXTRACT data extraction SAINT data reduction SADABS data scaling MOLREP phasing