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Polo-like kinase I Polo-box domain in complex with FDPPLHSpTA 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 6.5 293 100mM MES, 30% PEG 400, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2 38.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.969 α = 90 b = 88.658 β = 113.48 c = 67.59 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 2.38 62.02 99.4 25605 25445
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) 2.38 62.02 24149 1296 99.59 0.23509 0.23215 0.2415 0.28838 0.2963 RANDOM 40.886
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] -1.83 -1.49 1.03 -0.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.945 r_dihedral_angle_3_deg 17.171 r_dihedral_angle_4_deg 16.495 r_dihedral_angle_1_deg 5.232 r_scangle_it 1.201 r_angle_refined_deg 1.061 r_mcangle_it 1.003 r_scbond_it 0.732 r_mcbond_it 0.551 r_chiral_restr 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.945 r_dihedral_angle_3_deg 17.171 r_dihedral_angle_4_deg 16.495 r_dihedral_angle_1_deg 5.232 r_scangle_it 1.201 r_angle_refined_deg 1.061 r_mcangle_it 1.003 r_scbond_it 0.732 r_mcbond_it 0.551 r_chiral_restr 0.07 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 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 5435 Nucleic Acid Atoms Solvent Atoms 116 Heterogen Atoms 24
Software Software Software Name Purpose PHASER phasing REFMAC refinement