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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 = 120.806 α = 90 b = 120.806 β = 90 c = 238.587 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 IMAGE PLATE RIGAKU RAXIS IV 2004-08-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.54
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 2.6 43.69 100 0.053 28.7 9.7 32454 32450 -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 2.6 2.74 100 0.545 3.9 8.6 4648
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 2.6 43.69 32454 32450 1645 99.98 0.21147 0.21147 0.20955 0.2379 0.24795 0.2763 RANDOM 62.115
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] -0.11 -0.06 -0.11 0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.422 r_dihedral_angle_3_deg 20.201 r_dihedral_angle_4_deg 16.589 r_dihedral_angle_1_deg 6.444 r_scangle_it 3.879 r_scbond_it 2.396 r_angle_refined_deg 1.7 r_mcangle_it 1.547 r_mcbond_it 0.809 r_nbtor_refined 0.323
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.422 r_dihedral_angle_3_deg 20.201 r_dihedral_angle_4_deg 16.589 r_dihedral_angle_1_deg 6.444 r_scangle_it 3.879 r_scbond_it 2.396 r_angle_refined_deg 1.7 r_mcangle_it 1.547 r_mcbond_it 0.809 r_nbtor_refined 0.323 r_nbd_refined 0.25 r_metal_ion_refined 0.237 r_symmetry_vdw_refined 0.185 r_symmetry_hbond_refined 0.182 r_xyhbond_nbd_refined 0.164 r_chiral_restr 0.12 r_bond_refined_d 0.016 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 53 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling AMoRE phasing