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The polo-box domain of Plk1 in complex with a phospho-peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Unliganded polo box domain
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 PEG 20000, MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.54 51.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.071 α = 91.45 b = 56.888 β = 103.21 c = 85.05 γ = 118.5
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 QUANTUM 4 mirrors 2003-07-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.9792 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 29.36 95.7 0.068 0.096 2.7 1.9 38616 37228 49.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.3 2.42 96.6 0.364 0.258 2.1 1.9 5668
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 Unliganded polo box domain 2.3 29.36 36665 36665 1943 96.2 0.248 0.24832 0.24502 0.2368 0.31166 0.2935 RANDOM 44.646
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] 0.01 0.01 -0.01 0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.213 r_scangle_it 3.048 r_scbond_it 1.778 r_angle_refined_deg 1.591 r_mcangle_it 1.341 r_angle_other_deg 1.269 r_mcbond_it 0.707 r_symmetry_hbond_refined 0.337 r_symmetry_vdw_other 0.265 r_symmetry_vdw_refined 0.238
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.213 r_scangle_it 3.048 r_scbond_it 1.778 r_angle_refined_deg 1.591 r_mcangle_it 1.341 r_angle_other_deg 1.269 r_mcbond_it 0.707 r_symmetry_hbond_refined 0.337 r_symmetry_vdw_other 0.265 r_symmetry_vdw_refined 0.238 r_nbd_other 0.229 r_nbd_refined 0.201 r_xyhbond_nbd_refined 0.194 r_nbtor_other 0.094 r_chiral_restr 0.09 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5516 Nucleic Acid Atoms Solvent Atoms 191 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling MOLREP phasing