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Crystal structure of human CDK8-Cyclin C in complex with cortistatin A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3RGF PDB ENTRY 3RGF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 20% PEG3350, 0.2M LITHIUM CHLORIDE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K
Crystal Properties Matthews coefficient Solvent content 3.04 59.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.49 α = 90 b = 71.252 β = 90 c = 171.247 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 PIXEL DECTRIS PILATUS 6M 2012-07-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA SLS X06SA
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 2.4 85.62 94.9 0.07 2.8 34548 -3
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 2.4 2.65 98.6 0.45 2.8
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 3RGF 2.4 85.62 31676 1115 94.91 0.20095 0.19908 0.2082 0.25633 0.2606 RANDOM 31.69
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] -1.08 -0.1 1.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.016 r_dihedral_angle_4_deg 18.095 r_dihedral_angle_3_deg 12.464 r_long_range_B_refined 9.116 r_long_range_B_other 9.116 r_scangle_other 7.877 r_dihedral_angle_1_deg 5.949 r_mcangle_it 5.883 r_mcangle_other 5.883 r_scbond_it 5.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.016 r_dihedral_angle_4_deg 18.095 r_dihedral_angle_3_deg 12.464 r_long_range_B_refined 9.116 r_long_range_B_other 9.116 r_scangle_other 7.877 r_dihedral_angle_1_deg 5.949 r_mcangle_it 5.883 r_mcangle_other 5.883 r_scbond_it 5.46 r_scbond_other 5.454 r_mcbond_it 4.227 r_mcbond_other 4.227 r_angle_refined_deg 1.413 r_angle_other_deg 1.14 r_chiral_restr 0.089 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5017 Nucleic Acid Atoms Solvent Atoms 103 Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing