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Structure of the CDC25B Phosphatase Catalytic Domain with Bound Inhibitor
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, SITTING DROP 7.5 298 (NH4)2SO4, Tris, TCEP
Crystal Properties Matthews coefficient Solvent content 3.18 61.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.66 α = 90 b = 71.47 β = 90 c = 73.94 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 CCD MARMOSAIC 225 mm CCD 2014-06-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
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 1.33 51.39 100 0.098 10.5 3.6 63905
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 1.33 1.4 100 0.46 1.3 3.5
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 2A2K 1.5 51.39 42329 2226 99.98 0.1273 0.126 0.1258 0.15201 0.1522 RANDOM 19.655
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] -0.02 0.03 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.937 r_dihedral_angle_4_deg 22.274 r_sphericity_bonded 19.02 r_dihedral_angle_3_deg 12.318 r_rigid_bond_restr 8.932 r_dihedral_angle_1_deg 6.891 r_scangle_other 6.783 r_scbond_it 6.465 r_scbond_other 6.465 r_long_range_B_refined 6.167
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.937 r_dihedral_angle_4_deg 22.274 r_sphericity_bonded 19.02 r_dihedral_angle_3_deg 12.318 r_rigid_bond_restr 8.932 r_dihedral_angle_1_deg 6.891 r_scangle_other 6.783 r_scbond_it 6.465 r_scbond_other 6.465 r_long_range_B_refined 6.167 r_long_range_B_other 5.433 r_mcangle_it 3.407 r_mcangle_other 3.405 r_mcbond_other 3.033 r_mcbond_it 3.031 r_angle_refined_deg 1.928 r_angle_other_deg 1.422 r_chiral_restr 0.13 r_gen_planes_refined 0.015 r_bond_refined_d 0.012 r_gen_planes_other 0.01 r_bond_other_d 0.001 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_sphericity_free
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1472 Nucleic Acid Atoms Solvent Atoms 296 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling MOLREP phasing