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Molecular and structural basis of Plk1 substrate recognition: Implications in centrosomal localization
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UMW PDB ENTRY 1UMW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 9 289 0.1 M Sodium Chloride, 0.1 M Bicine, 20% w/v Polyethylene Glycol Monomethyl Ether 550, pH 9.0, VAPOR DIFFUSION, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.3 46.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.051 α = 90 b = 99.017 β = 90 c = 33.19 γ = 90
Symmetry Space Group P 21 21 2
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 2005-05-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.95 55 93.94 0.06 3.4 16920 16920 10.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.95 2.05 99.9 0.36 1.3 3.2
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 1UMW 1.95 60.86 16905 922 93.33 0.16219 0.15914 0.1621 0.22125 0.2228 RANDOM 22.542
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] -0.04 0.03 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.086 r_dihedral_angle_4_deg 23.393 r_dihedral_angle_3_deg 15.56 r_scangle_it 7.752 r_dihedral_angle_1_deg 7.069 r_scbond_it 5.678 r_mcangle_it 3.172 r_mcbond_it 2.195 r_angle_refined_deg 1.951 r_symmetry_vdw_refined 0.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.086 r_dihedral_angle_4_deg 23.393 r_dihedral_angle_3_deg 15.56 r_scangle_it 7.752 r_dihedral_angle_1_deg 7.069 r_scbond_it 5.678 r_mcangle_it 3.172 r_mcbond_it 2.195 r_angle_refined_deg 1.951 r_symmetry_vdw_refined 0.5 r_nbtor_refined 0.313 r_xyhbond_nbd_refined 0.252 r_nbd_refined 0.247 r_symmetry_hbond_refined 0.243 r_chiral_restr 0.168 r_bond_refined_d 0.025 r_gen_planes_refined 0.008 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1722 Nucleic Acid Atoms Solvent Atoms 193 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing