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Crystal Structure of DDB1 in Complex with the H-Box Motif of WDR42A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2B5M PDB ENTRY 2B5M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 16% PEG 4000, 0.2M SODIUM CHLORIDE, 0.1M MES, 0.005M DTT , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.06 59.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.138 α = 90 b = 133.815 β = 90.45 c = 183.999 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 173 CCD ADSC QUANTUM 315 2008-05-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.0,1.005 ALS 5.0.2
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 3.4 49.15 91.9 0.142 10.7 3.1 38723 35597 2 1
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 3.4 3.488 92.6 0.541 2.4 2592
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 2B5M 3.4 49.15 2 38723 35597 1826 87.32 0.304 0.264 0.26 0.249 0.338 0.2476 RANDOM 77.285
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] -1.86 0.11 1.83 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.396 r_dihedral_angle_3_deg 19.966 r_dihedral_angle_4_deg 19.681 r_dihedral_angle_1_deg 6.53 r_angle_refined_deg 1.264 r_scangle_it 0.921 r_mcangle_it 0.701 r_scbond_it 0.529 r_mcbond_it 0.39 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.396 r_dihedral_angle_3_deg 19.966 r_dihedral_angle_4_deg 19.681 r_dihedral_angle_1_deg 6.53 r_angle_refined_deg 1.264 r_scangle_it 0.921 r_mcangle_it 0.701 r_scbond_it 0.529 r_mcbond_it 0.39 r_nbtor_refined 0.307 r_nbd_refined 0.22 r_symmetry_hbond_refined 0.209 r_symmetry_vdw_refined 0.161 r_xyhbond_nbd_refined 0.158 r_chiral_restr 0.08 r_bond_refined_d 0.008 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 17652 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling