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Crystal Structure of DDB1 in Complex with the H-Box Motif of WDR40A
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 2.99 58.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.599 α = 90 b = 132.522 β = 90 c = 183.052 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 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 45.79 90.3 0.079 27.7 4.2 29177 26351 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) 3 3.078 89.5 0.401 3.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 2B5M 3 45.79 29177 26351 1336 87.04 0.24247 0.23952 0.2514 0.30119 0.2463 RANDOM 80.631
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] -0.82 1.12 -0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.265 r_dihedral_angle_3_deg 22.371 r_dihedral_angle_4_deg 19.625 r_dihedral_angle_1_deg 8.304 r_angle_refined_deg 1.933 r_nbtor_refined 0.33 r_symmetry_hbond_refined 0.298 r_nbd_refined 0.289 r_xyhbond_nbd_refined 0.231 r_symmetry_vdw_refined 0.204
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.265 r_dihedral_angle_3_deg 22.371 r_dihedral_angle_4_deg 19.625 r_dihedral_angle_1_deg 8.304 r_angle_refined_deg 1.933 r_nbtor_refined 0.33 r_symmetry_hbond_refined 0.298 r_nbd_refined 0.289 r_xyhbond_nbd_refined 0.231 r_symmetry_vdw_refined 0.204 r_chiral_restr 0.116 r_bond_refined_d 0.017 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_scbond_it r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8842 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