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X-ray structure of mouse pyrimidine 5'-nucleotidase type 1, product-transition complex analog with Aluminum 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 aluminum chloride, 0.050 M sodium fluoride, 0.010 M uridine, vapor diffusion, hanging drop, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.01 59.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 135.044 α = 90 b = 135.044 β = 90 c = 39.049 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 2005-12-18 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 67.52 99.9 0.0991 19.01 16.69 33163
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 0.7363 1.94 6.08 2039
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 67.52 33031 1673 99.563 0.194 0.194 0.1901 0.1889 0.2603 0.255 RANDOM 43.413
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] 0.858 0.429 0.858 -1.287
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.893 r_dihedral_angle_4_deg 22.124 r_dihedral_angle_3_deg 16.836 r_dihedral_angle_1_deg 6.467 r_scangle_it 2.875 r_scbond_it 1.923 r_angle_refined_deg 1.407 r_mcangle_it 1.122 r_mcbond_it 0.701 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.893 r_dihedral_angle_4_deg 22.124 r_dihedral_angle_3_deg 16.836 r_dihedral_angle_1_deg 6.467 r_scangle_it 2.875 r_scbond_it 1.923 r_angle_refined_deg 1.407 r_mcangle_it 1.122 r_mcbond_it 0.701 r_nbtor_refined 0.304 r_nbd_refined 0.205 r_xyhbond_nbd_refined 0.18 r_symmetry_vdw_refined 0.162 r_symmetry_hbond_refined 0.121 r_chiral_restr 0.104 r_metal_ion_refined 0.056 r_bond_refined_d 0.015 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4652 Nucleic Acid Atoms Solvent Atoms 479 Heterogen Atoms 10
Software Software Software Name Purpose SAINT data scaling REFMAC refinement PDB_EXTRACT data extraction SAINT data reduction SADABS data scaling MOLREP phasing