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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 = 120.752 α = 90 b = 120.752 β = 90 c = 239.153 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 2.48 50 99.8 0.038 54.6 11.3 37333 37232 -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 2.48 2.57 100 0.749 3.5 9.1 3657
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 2.48 50 37232 35738 1494 99.73 0.21105 0.21105 0.2101 0.2607 0.234 0.2786 RANDOM 64.054
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] -0.08 -0.04 -0.08 0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.532 r_dihedral_angle_3_deg 19.327 r_dihedral_angle_4_deg 17.301 r_dihedral_angle_1_deg 6.531 r_scangle_it 3.975 r_scbond_it 2.557 r_angle_refined_deg 1.685 r_mcangle_it 1.429 r_mcbond_it 0.741 r_nbtor_refined 0.318
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.532 r_dihedral_angle_3_deg 19.327 r_dihedral_angle_4_deg 17.301 r_dihedral_angle_1_deg 6.531 r_scangle_it 3.975 r_scbond_it 2.557 r_angle_refined_deg 1.685 r_mcangle_it 1.429 r_mcbond_it 0.741 r_nbtor_refined 0.318 r_nbd_refined 0.241 r_symmetry_vdw_refined 0.195 r_metal_ion_refined 0.184 r_symmetry_hbond_refined 0.163 r_xyhbond_nbd_refined 0.128 r_chiral_restr 0.117 r_bond_refined_d 0.019 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 3790 Nucleic Acid Atoms Solvent Atoms 67 Heterogen Atoms 41
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing