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Human Plk1-PBD in complex with Thymoquinone at the phophopeptide binding site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UMW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 291 1.4M Sodium Potassium Tartrate, 50mM MES pH 6.5, 100mM Hepes pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.08 40.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.26 α = 90 b = 102.15 β = 93.96 c = 67.74 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 100 IMAGE PLATE MAR scanner 345 mm plate 2009-05-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.5418
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 2.75 51.07 94.6 0.154 5.3 2.4 11125
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 2.75 2.9 91.5 0.387 2.8 2 1551
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 2.75 51.07 10576 531 94.18 0.20956 0.20588 0.204 0.2802 0.2773 RANDOM 15.541
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] -0.11 0.04 0.04 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.402 r_dihedral_angle_4_deg 20.312 r_dihedral_angle_3_deg 16.758 r_dihedral_angle_1_deg 5.742 r_scangle_it 1.511 r_angle_refined_deg 1.126 r_scbond_it 0.896 r_mcangle_it 0.711 r_mcbond_it 0.374 r_chiral_restr 0.076
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.402 r_dihedral_angle_4_deg 20.312 r_dihedral_angle_3_deg 16.758 r_dihedral_angle_1_deg 5.742 r_scangle_it 1.511 r_angle_refined_deg 1.126 r_scbond_it 0.896 r_mcangle_it 0.711 r_mcbond_it 0.374 r_chiral_restr 0.076 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 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 3519 Nucleic Acid Atoms Solvent Atoms 103 Heterogen Atoms 18
Software Software Software Name Purpose MAR345dtb data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling