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Crystal structure of the PDK3-L2 complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JM6 PDK2 PDB entry 1JM6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 293 soudium citrate, sodium potassium phosphate, sodium chrolide, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 4.7 73.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.904 α = 90 b = 120.904 β = 90 c = 240.085 γ = 120
Symmetry Space Group P 65 2 2
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 QUANTUM 310 2003-08-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97 APS 19-ID
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 2.62 50 98.4 0.059 30 7.5 31538 31043 -3
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 2.62 2.71 97.2 0.542 2.1 5.1 2970
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 (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 PDK2 PDB entry 1JM6 2.63 50 31043 29477 1566 98.34 0.20495 0.20495 0.20358 0.2584 0.2302 0.2789 RANDOM 66.251
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] -0.79 -0.39 -0.79 1.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.041 r_dihedral_angle_3_deg 20.209 r_dihedral_angle_4_deg 17.618 r_dihedral_angle_1_deg 6.37 r_scangle_it 3.572 r_scbond_it 2.201 r_angle_refined_deg 1.731 r_mcangle_it 1.297 r_mcbond_it 0.679 r_nbtor_refined 0.322
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.041 r_dihedral_angle_3_deg 20.209 r_dihedral_angle_4_deg 17.618 r_dihedral_angle_1_deg 6.37 r_scangle_it 3.572 r_scbond_it 2.201 r_angle_refined_deg 1.731 r_mcangle_it 1.297 r_mcbond_it 0.679 r_nbtor_refined 0.322 r_nbd_refined 0.25 r_symmetry_vdw_refined 0.21 r_metal_ion_refined 0.182 r_symmetry_hbond_refined 0.151 r_xyhbond_nbd_refined 0.134 r_chiral_restr 0.111 r_bond_refined_d 0.015 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_other r_symmetry_vdw_other r_symmetry_hbond_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3836 Nucleic Acid Atoms Solvent Atoms 56 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing