☰ Navigation Tabs
X-ray structure of mouse pyrimidine 5'-nucleotidase type 1, product complex
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 60 MINUTES IN WELL SOLUTION WITH 0.005 M magnesium chloride, 0.005 M UMP, temperature 277K, VAPOR DIFFUSION, HANGING DROP, pH 6.00
Crystal Properties Matthews coefficient Solvent content 2.96 58.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 134.006 α = 90 b = 134.006 β = 90 c = 39.087 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 ADSC QUANTUM 315 2005-11-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 8-BM APS 8-BM
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 2.1 50 98.9 0.071 13.11 3.8 45396
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 2.1 2.15 97.6 0.342 3.42 3.2
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2BDU 2.1 32.19 45392 2257 98.9 0.153 0.15 0.1645 0.198 0.1846 RANDOM 38.09
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 39.322 r_dihedral_angle_4_deg 20.609 r_dihedral_angle_3_deg 14.187 r_dihedral_angle_1_deg 5.492 r_scangle_it 5.043 r_scbond_it 3.867 r_mcangle_it 1.918 r_angle_refined_deg 1.316 r_mcbond_it 1.141 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.322 r_dihedral_angle_4_deg 20.609 r_dihedral_angle_3_deg 14.187 r_dihedral_angle_1_deg 5.492 r_scangle_it 5.043 r_scbond_it 3.867 r_mcangle_it 1.918 r_angle_refined_deg 1.316 r_mcbond_it 1.141 r_nbtor_refined 0.304 r_symmetry_vdw_refined 0.204 r_nbd_refined 0.193 r_symmetry_hbond_refined 0.178 r_xyhbond_nbd_refined 0.172 r_chiral_restr 0.093 r_bond_refined_d 0.015 r_gen_planes_refined 0.005 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_refined 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4652 Nucleic Acid Atoms Solvent Atoms 848 Heterogen Atoms 48
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction MOLREP phasing