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1.1A X-RAY STRUCTURE OF THE APO CATALYTIC DOMAIN OF DEATH-ASSOCIATED PROTEIN KINASE 1, aa 1-277
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2W4J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 292 0.1 M HEPES, Ph=7, 2M Ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 1.99 38.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.516 α = 90 b = 62.005 β = 90 c = 88.375 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 100 PIXEL DECTRIS PILATUS 6M-F 2014-04-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.973 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 1.129 50.758 99.4 0.076 0.082 0.032 10.7 6.3 96009 96009
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.13 1.19 96.5 0.709 0.709 0.341 1.1 5 13431
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 2W4J 1.13 50.758 95914 4805 99.36 0.1183 0.1167 0.1194 0.1495 0.149 RANDOM 16.198
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] -1.09 0.61 0.49
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 36.855 r_dihedral_angle_2_deg 36.204 r_dihedral_angle_4_deg 21.611 r_sphericity_bonded 17.943 r_dihedral_angle_3_deg 12.907 r_rigid_bond_restr 6.955 r_dihedral_angle_1_deg 6.164 r_angle_refined_deg 2.184 r_angle_other_deg 2.168 r_chiral_restr 0.163
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 36.855 r_dihedral_angle_2_deg 36.204 r_dihedral_angle_4_deg 21.611 r_sphericity_bonded 17.943 r_dihedral_angle_3_deg 12.907 r_rigid_bond_restr 6.955 r_dihedral_angle_1_deg 6.164 r_angle_refined_deg 2.184 r_angle_other_deg 2.168 r_chiral_restr 0.163 r_bond_refined_d 0.024 r_gen_planes_refined 0.012 r_gen_planes_other 0.005 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2232 Nucleic Acid Atoms Solvent Atoms 489 Heterogen Atoms 107
Software Software Software Name Purpose SCALA data scaling MOLREP phasing PDB_EXTRACT data extraction REFMAC refinement XDS data reduction XSCALE data reduction