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X-ray structure of mouse pyrimidine 5'-nucleotidase type 1, with bound magnesium(II)
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 15 MINUTES IN WELL SOLUTION WITH 0.005 M magnesium chloride, temperature 277K, VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 2.98 58.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 134.343 α = 90 b = 134.343 β = 90 c = 39.152 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 2006-01-03 M 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 2.25 67.17 100 0.1006 20.61 17.82 37523
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 2.25 2.3 100 0.6371 2.67 6.47 2423
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 2.25 67.17 37505 1899 99.955 0.158 0.158 0.1548 0.1543 0.2193 0.2185 RANDOM 35.072
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] 0.204 0.102 0.204 -0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.774 r_dihedral_angle_4_deg 22.555 r_dihedral_angle_3_deg 15.516 r_scangle_it 5.969 r_dihedral_angle_1_deg 5.893 r_scbond_it 4.389 r_mcangle_it 2.236 r_angle_refined_deg 1.474 r_mcbond_it 1.291 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.774 r_dihedral_angle_4_deg 22.555 r_dihedral_angle_3_deg 15.516 r_scangle_it 5.969 r_dihedral_angle_1_deg 5.893 r_scbond_it 4.389 r_mcangle_it 2.236 r_angle_refined_deg 1.474 r_mcbond_it 1.291 r_nbtor_refined 0.309 r_symmetry_vdw_refined 0.249 r_xyhbond_nbd_refined 0.212 r_nbd_refined 0.207 r_symmetry_hbond_refined 0.193 r_chiral_restr 0.107 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 815 Heterogen Atoms 38
Software Software Software Name Purpose SAINT data scaling REFMAC refinement PDB_EXTRACT data extraction SAINT data reduction SADABS data scaling MOLREP phasing