☰ Navigation Tabs
Structure of the PDK1 PH domain K465E mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1W1D PDB ENTRY 1W1D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 0.2 M LITHIUM SULPHATE, 0.1 M TRIS HYDROCHLORIDE [PH 8.5] 30 % (W/V) PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.2 44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.009 α = 90 b = 67.057 β = 90 c = 67.802 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 IMAGE PLATE RIGAKU IMAGE PLATE 2004-06-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007
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 1.8 25 100 0.06 10 4.5 14950 2
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 1.8 1.86 100 0.55 2.3 4.3
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 1W1D 1.8 25 14309 609 99.5 0.175 0.173 0.1862 0.215 0.2253 RANDOM 21.05
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] 0.12 -0.64 0.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.298 r_scangle_it 4.059 r_scbond_it 2.542 r_mcangle_it 1.78 r_angle_refined_deg 1.681 r_mcbond_it 0.983 r_angle_other_deg 0.904 r_symmetry_vdw_other 0.312 r_nbd_other 0.253 r_nbd_refined 0.216
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.298 r_scangle_it 4.059 r_scbond_it 2.542 r_mcangle_it 1.78 r_angle_refined_deg 1.681 r_mcbond_it 0.983 r_angle_other_deg 0.904 r_symmetry_vdw_other 0.312 r_nbd_other 0.253 r_nbd_refined 0.216 r_symmetry_vdw_refined 0.19 r_xyhbond_nbd_refined 0.16 r_symmetry_hbond_refined 0.117 r_chiral_restr 0.106 r_nbtor_other 0.086 r_bond_refined_d 0.016 r_gen_planes_other 0.011 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other 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 1172 Nucleic Acid Atoms Solvent Atoms 112 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing