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THE CRYSTAL STRUCTURE OF THE UBIQUITIN-LIKE (UBL) DOMAIN OF HHR23A (HUMAN HOMOLOGUE A OF RAD23)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BWF PDB ENTRY 2BWF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 0.1 M HEPES PH 7.5, 2% PEG 400 AND 2.0 M AMMONIUM SULFATE, AT ROOM TEMPERATURE
Crystal Properties Matthews coefficient Solvent content 3.04 59.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.434 α = 90 b = 78.434 β = 90 c = 63.472 γ = 120
Symmetry Space Group P 65 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 CCD 2009-09-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 Diamond I04
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 1.65 63.57 100 0.08 5.86 36.17 14363 2 21.4
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 1.65 1.74 100 0.35 2.08 23
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2BWF 1.651 35 14330 706 99.902 0.126 0.1241 0.1598 0.2359 RANDOM 9.296
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] 0.026 0.013 0.026 -0.039
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.598 r_dihedral_angle_4_deg 22.156 r_sphericity_free 20.126 r_dihedral_angle_3_deg 14.992 r_scangle_it 7.41 r_dihedral_angle_1_deg 6.351 r_sphericity_bonded 5.566 r_scbond_it 5.423 r_mcangle_it 3.553 r_angle_other_deg 3.113
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.598 r_dihedral_angle_4_deg 22.156 r_sphericity_free 20.126 r_dihedral_angle_3_deg 14.992 r_scangle_it 7.41 r_dihedral_angle_1_deg 6.351 r_sphericity_bonded 5.566 r_scbond_it 5.423 r_mcangle_it 3.553 r_angle_other_deg 3.113 r_mcbond_it 2.576 r_rigid_bond_restr 2.479 r_angle_refined_deg 2.288 r_mcbond_other 1.171 r_nbd_refined 0.299 r_chiral_restr 0.276 r_symmetry_hbond_refined 0.273 r_xyhbond_nbd_refined 0.269 r_symmetry_vdw_refined 0.218 r_nbd_other 0.189 r_nbtor_refined 0.168 r_symmetry_vdw_other 0.147 r_nbtor_other 0.095 r_bond_refined_d 0.029 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 r_bond_other_d 0.001 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 603 Nucleic Acid Atoms Solvent Atoms 108 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing