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The structure of UBR box (KIAA)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NIS PDB ENTRY 3NIS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 295 0.16M ammonium acetate, 0.01M calcium chloride dihydrate, 0.05M sodium cacodylate trihydrate pH 6.5, 8%(w/v) PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.81 56.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.153 α = 90 b = 58.153 β = 90 c = 110.856 γ = 120
Symmetry Space Group P 61 2 2
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 210 2009-03-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 4A 1.0000 PAL/PLS 4A
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 99.8 0.069 13.1 23.7 7052
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) 2.1 2.18 100 0.462 21.1 668
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 3NIS 2.1 24.56 6960 332 99.87 0.2526 0.2512 0.267 0.2815 0.277 RANDOM 55.462
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] -0.14 -0.07 -0.14 0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.872 r_dihedral_angle_3_deg 16.056 r_dihedral_angle_4_deg 11.717 r_dihedral_angle_1_deg 4.75 r_scangle_it 1.24 r_angle_refined_deg 0.925 r_scbond_it 0.72 r_mcangle_it 0.659 r_mcbond_it 0.397 r_symmetry_vdw_refined 0.317
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.872 r_dihedral_angle_3_deg 16.056 r_dihedral_angle_4_deg 11.717 r_dihedral_angle_1_deg 4.75 r_scangle_it 1.24 r_angle_refined_deg 0.925 r_scbond_it 0.72 r_mcangle_it 0.659 r_mcbond_it 0.397 r_symmetry_vdw_refined 0.317 r_nbtor_refined 0.292 r_nbd_refined 0.176 r_xyhbond_nbd_refined 0.14 r_chiral_restr 0.075 r_symmetry_hbond_refined 0.071 r_metal_ion_refined 0.059 r_bond_refined_d 0.007 r_gen_planes_refined 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 640 Nucleic Acid Atoms Solvent Atoms 22 Heterogen Atoms 3
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing