☰ Navigation Tabs
Polo-like kinase I Polo-box domain in complex with DPPLHSpTA phosphopeptide from PBIP1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UMW 1UMW (chain A)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.2 293 100mM Na/K phosphate, 0.2M NaCl, 10% PEG 8000, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.95 36.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.931 α = 90 b = 50.116 β = 99.31 c = 58.73 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 2010-04-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.9334 ESRF ID14-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.59 57.93 99.4 27774 27603
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 1UMW (chain A) 1.59 57.93 26218 1385 99.4 0.19757 0.19465 0.1933 0.25237 0.2515 RANDOM 22.027
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.697 r_dihedral_angle_4_deg 24.866 r_dihedral_angle_3_deg 16.381 r_dihedral_angle_1_deg 6.825 r_scangle_it 5.052 r_scbond_it 3.511 r_mcangle_it 2.514 r_angle_refined_deg 2.255 r_mcbond_it 1.519 r_chiral_restr 0.193
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.697 r_dihedral_angle_4_deg 24.866 r_dihedral_angle_3_deg 16.381 r_dihedral_angle_1_deg 6.825 r_scangle_it 5.052 r_scbond_it 3.511 r_mcangle_it 2.514 r_angle_refined_deg 2.255 r_mcbond_it 1.519 r_chiral_restr 0.193 r_bond_refined_d 0.025 r_gen_planes_refined 0.012 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_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 1804 Nucleic Acid Atoms Solvent Atoms 189 Heterogen Atoms 11
Software Software Software Name Purpose MOLREP phasing REFMAC refinement