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CRYSTAL STRUCTURE OF WILD-TYPE PLK-1 KINASE DOMAIN IN COMPLEX WITH A SELECTIVE DARPIN
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OL5 PLK-1 - HOMOLOGY MODEL FROM PDB ENTRY 1OL5 DARPIN 3H10 - PDB ENTRY 1MJ0 TRUNCATED AFTER RESIDUE 141 experimental model PDB 3H10 PLK-1 - HOMOLOGY MODEL FROM PDB ENTRY 1OL5 DARPIN 3H10 - PDB ENTRY 1MJ0 TRUNCATED AFTER RESIDUE 141 experimental model PDB 1MJ0 PLK-1 - HOMOLOGY MODEL FROM PDB ENTRY 1OL5 DARPIN 3H10 - PDB ENTRY 1MJ0 TRUNCATED AFTER RESIDUE 141
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 303 0.1 M TRIS-HCL PH 8.0, 8% PEG 5000 MME, 0.01 M EDTA SODIUM SALT AT 303 K.
Crystal Properties Matthews coefficient Solvent content 2.7 54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.329 α = 90 b = 135.225 β = 90 c = 136.824 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 CCD ADSC CCD MIRRORS 2006-07-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 ESRF ID29
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 2.3 96.2 99.3 0.06 15.7 3.5 51702 45.7
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 2.3 2.42 99.3 0.4 3.3 3.6
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PLK-1 - HOMOLOGY MODEL FROM PDB ENTRY 1OL5 DARPIN 3H10 - PDB ENTRY 1MJ0 TRUNCATED AFTER RESIDUE 141 2.3 61.08 49051 2601 98.9 0.184 0.182 0.224 RANDOM 34.28
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] 1.07 -1.87 0.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.477 r_dihedral_angle_4_deg 18.875 r_dihedral_angle_3_deg 15.116 r_scangle_it 7.068 r_dihedral_angle_1_deg 5.952 r_scbond_it 5.214 r_mcangle_it 2.8 r_mcbond_it 1.615 r_angle_refined_deg 1.265 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.477 r_dihedral_angle_4_deg 18.875 r_dihedral_angle_3_deg 15.116 r_scangle_it 7.068 r_dihedral_angle_1_deg 5.952 r_scbond_it 5.214 r_mcangle_it 2.8 r_mcbond_it 1.615 r_angle_refined_deg 1.265 r_nbtor_refined 0.307 r_symmetry_vdw_refined 0.207 r_nbd_refined 0.199 r_symmetry_hbond_refined 0.162 r_xyhbond_nbd_refined 0.144 r_chiral_restr 0.087 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 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_refined r_metal_ion_other r_symmetry_vdw_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 6502 Nucleic Acid Atoms Solvent Atoms 406 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing