☰ Navigation Tabs
CDK2/cyclin A2 in complex with 3H-pyrazolo[4,3-f]quinoline-based derivative HSD1368
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6GVA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 80% Morpheus condition 35 containing: 10% w/v PEG 4,000, 20% v/v glycerol, 0.03 M NaNO3, 0.03 M Na2HPO4, 0.03 M (NH4)2SO4, 0.1 M Tris/Bicine pH 8.5 and 20% of JCSG+ condition 59 containing: 14.4 % w/v PEG 8,000, 20% v/v Glycerol, 0.16 M calcium acetate, 0.08 M sodium cacodylate pH 6.5
Crystal Properties Matthews coefficient Solvent content 3.19 61.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.077 α = 90 b = 164.7 β = 106.28 c = 73.411 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 PIXEL DECTRIS PILATUS 6M 2020-06-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.918 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) 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 2.54 47.1 84 0.309 0.342 0.968 5.35 5.502 43971 35.409
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.54 2.7 69.2 1.429 1.599 0.468 1 4.762
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 6gva 2.54 47.1 41850 2129 84.07 0.2482 0.246 0.2493 0.2906 0.2909 RANDOM 37.521
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] 6 2.37 -3.52 -3.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.587 r_dihedral_angle_4_deg 17.018 r_dihedral_angle_3_deg 16.232 r_dihedral_angle_1_deg 6.606 r_angle_other_deg 2.246 r_angle_refined_deg 1.623 r_chiral_restr 0.07 r_bond_other_d 0.034 r_bond_refined_d 0.011 r_gen_planes_other 0.009
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.587 r_dihedral_angle_4_deg 17.018 r_dihedral_angle_3_deg 16.232 r_dihedral_angle_1_deg 6.606 r_angle_other_deg 2.246 r_angle_refined_deg 1.623 r_chiral_restr 0.07 r_bond_other_d 0.034 r_bond_refined_d 0.011 r_gen_planes_other 0.009 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8729 Nucleic Acid Atoms Solvent Atoms 77 Heterogen Atoms 73
Software Software Software Name Purpose XDS data reduction XSCALE data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction