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Crystal Structure of DDB1 in Complex with the H-Box Motif of DDB2
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, 0.005 M DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.03 59.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.78 α = 90 b = 134.149 β = 90 c = 182.561 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 2.8 48.74 91.2 0.091 24.3 39401 35953 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) 2.8 2.87 86.3 0.589 2.6 2427
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 2.8 48.74 2 39401 35953 1894 95.97 0.269 0.249 0.247 0.2515 0.289 0.2636 RANDOM 77.702
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] -1.72 -2.32 4.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.114 r_dihedral_angle_3_deg 21.069 r_dihedral_angle_4_deg 17.336 r_dihedral_angle_1_deg 7.093 r_angle_refined_deg 1.649 r_nbtor_refined 0.32 r_nbd_refined 0.261 r_xyhbond_nbd_refined 0.197 r_symmetry_vdw_refined 0.18 r_chiral_restr 0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.114 r_dihedral_angle_3_deg 21.069 r_dihedral_angle_4_deg 17.336 r_dihedral_angle_1_deg 7.093 r_angle_refined_deg 1.649 r_nbtor_refined 0.32 r_nbd_refined 0.261 r_xyhbond_nbd_refined 0.197 r_symmetry_vdw_refined 0.18 r_chiral_restr 0.11 r_symmetry_hbond_refined 0.078 r_bond_refined_d 0.015 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8840 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