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Structure of hUPP2 in an active conformation with bound 5-benzylacyclouridine
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 277 2.0M ammonium sulfate, 0.1 M Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.72 54.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 275.342 α = 90 b = 56.137 β = 96.38 c = 141.389 γ = 90
Symmetry Space Group C 1 2 1
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 2010-07-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL7-1 0.98 SSRL BL7-1
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 50 92.4 0.153 9.1 2.3 134252
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 2.07 54.3 0.4 1.3 7819
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2 35.44 134248 6734 92.11 0.2069 0.205 0.2039 0.2418 0.2405 RANDOM 33.1254
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] -0.7 -1.05 1.72 -1.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.108 r_dihedral_angle_4_deg 17.36 r_dihedral_angle_3_deg 13.759 r_dihedral_angle_1_deg 5.897 r_scangle_it 4.034 r_scbond_it 2.8 r_mcangle_it 1.569 r_angle_refined_deg 1.475 r_mcbond_it 1.385 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.108 r_dihedral_angle_4_deg 17.36 r_dihedral_angle_3_deg 13.759 r_dihedral_angle_1_deg 5.897 r_scangle_it 4.034 r_scbond_it 2.8 r_mcangle_it 1.569 r_angle_refined_deg 1.475 r_mcbond_it 1.385 r_nbtor_refined 0.308 r_nbd_refined 0.204 r_symmetry_hbond_refined 0.169 r_symmetry_vdw_refined 0.157 r_xyhbond_nbd_refined 0.152 r_chiral_restr 0.095 r_bond_refined_d 0.015 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13496 Nucleic Acid Atoms Solvent Atoms 359 Heterogen Atoms 150
Software Software Software Name Purpose SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction ADSC data collection DENZO data reduction