☰ Navigation Tabs
X-ray structure of the complex between the catalytic domain of CDC25B C473S and 3-O-methylfluorescein phosphate (3-OMFP)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2A2K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 3.8 M NaCl, 0.1 M HEPES pH 7.5, and 1.2% v/v 2-propanol
Crystal Properties Matthews coefficient Solvent content 2.79 55.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.538 α = 90 b = 66.318 β = 90 c = 68.397 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 2M 2020-09-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.0000 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.04 47.61 98.6 1 15.3 11.4 16632
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.04 2.1 87.5 0.5 1.4 5.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.04 43.61 15694 817 97.99 0.19592 0.1949 0.1949 0.21425 0.2144 RANDOM 36.929
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] 0.09 -0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 17.242 r_dihedral_angle_3_deg 12.886 r_long_range_B_refined 8.52 r_dihedral_angle_1_deg 6.584 r_mcangle_it 4.15 r_scbond_it 3.415 r_mcbond_it 2.567 r_angle_refined_deg 1.43 r_chiral_restr 0.111 r_gen_planes_refined 0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 17.242 r_dihedral_angle_3_deg 12.886 r_long_range_B_refined 8.52 r_dihedral_angle_1_deg 6.584 r_mcangle_it 4.15 r_scbond_it 3.415 r_mcbond_it 2.567 r_angle_refined_deg 1.43 r_chiral_restr 0.111 r_gen_planes_refined 0.005 r_bond_refined_d 0.004 r_bond_other_d r_angle_other_deg r_dihedral_angle_4_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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1520 Nucleic Acid Atoms Solvent Atoms 119 Heterogen Atoms 63
Software Software Software Name Purpose XDS data reduction Aimless data scaling autoPROC data processing PHASER phasing REFMAC refinement PDB_EXTRACT data extraction