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Crystal structure of the UBL domain of Dsk2 from S. cerevisiae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BT0 PDB ENTRY 1BT0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 pH 7.00
Crystal Properties Matthews coefficient Solvent content 2 38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.415 α = 90 b = 49.587 β = 90 c = 58.771 γ = 90
Symmetry Space Group P 21 21 21
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 CCD 2002-12-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
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 1.15 37.8 93.8 0.08 3.6 4.5 48617 6
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 1.15 1.21 81.2 0.29 2.3 2.5
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1BT0 1.15 34.92 46148 2465 93.5 0.185 0.184 0.1912 0.195 RANDOM 11.83
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] 0.24 -0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.544 r_scangle_it 3.937 r_scbond_it 2.431 r_mcangle_it 1.907 r_angle_refined_deg 1.369 r_mcbond_it 1.246 r_angle_other_deg 0.721 r_symmetry_vdw_other 0.357 r_nbd_other 0.242 r_nbd_refined 0.194
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.544 r_scangle_it 3.937 r_scbond_it 2.431 r_mcangle_it 1.907 r_angle_refined_deg 1.369 r_mcbond_it 1.246 r_angle_other_deg 0.721 r_symmetry_vdw_other 0.357 r_nbd_other 0.242 r_nbd_refined 0.194 r_symmetry_vdw_refined 0.159 r_symmetry_hbond_refined 0.151 r_xyhbond_nbd_refined 0.116 r_nbtor_other 0.084 r_chiral_restr 0.081 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_gen_planes_other 0.003 r_bond_other_d 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1210 Nucleic Acid Atoms Solvent Atoms 159 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling AMoRE phasing