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Dimeric structure of DAPK-1 catalytic domain in complex with AMPPCP- Mg
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2W4J PDB ENTRY 2W4J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 0.1 M HEPES PH7.0, 0.1M MGCL2, 15% PEG4000
Crystal Properties Matthews coefficient Solvent content 2.95 58.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.407 α = 90 b = 76.578 β = 92.01 c = 106.892 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 100 CCD ADSC CCD MIRRORS 2011-03-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 ESRF ID29
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 2.65 45.71 99.8 0.08 10.2 4 39321 2.5
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 2.65 2.79 97.4 0.47 2.5 4
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 2W4J 2.65 106.83 37331 1976 99.81 0.21947 0.21601 0.2158 0.2846 0.2836 RANDOM 56.865
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] -3.04 0.33 5.96 -2.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.775 r_dihedral_angle_4_deg 21.08 r_dihedral_angle_3_deg 20.897 r_dihedral_angle_1_deg 7.255 r_angle_refined_deg 1.756 r_chiral_restr 0.105 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.775 r_dihedral_angle_4_deg 21.08 r_dihedral_angle_3_deg 20.897 r_dihedral_angle_1_deg 7.255 r_angle_refined_deg 1.756 r_chiral_restr 0.105 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7674 Nucleic Acid Atoms Solvent Atoms 128 Heterogen Atoms 130
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing