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Structural mechanism for the inhibition of CD5-p25 from the roscovitine, aloisine and indirubin.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1H4L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 13% PEG 3350, 0.1 M KI, 0.1 M BISTRISPROPANE PH 7.0, 10 MM DTT
Crystal Properties Matthews coefficient Solvent content 2.8 56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.988 α = 90 b = 117.988 β = 90 c = 156.167 γ = 120
Symmetry Space Group P 32 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 287 CCD ADSC CCD 2002-09-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
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 2.2 25 94.6 0.011 8.9 8.8 64818 2.5
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 2.2 2.3 97.7 0.37 2.8 3
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 1H4L 2.2 19.76 57534 3057 94.4 0.216 0.216 0.2184 0.219 0.226 RANDOM 23.02
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] 0.35 0.17 0.35 -0.52
RMS Deviations Key Refinement Restraint Deviation r_chiral_restr 6.273 r_dihedral_angle_3_deg 3.71 r_scangle_it 2.899 r_scbond_it 1.885 r_angle_other_deg 1.541 r_mcangle_it 1.159 r_mcbond_it 0.659 r_symmetry_vdw_other 0.348 r_symmetry_vdw_refined 0.292 r_nbd_other 0.27
RMS Deviations Key Refinement Restraint Deviation r_chiral_restr 6.273 r_dihedral_angle_3_deg 3.71 r_scangle_it 2.899 r_scbond_it 1.885 r_angle_other_deg 1.541 r_mcangle_it 1.159 r_mcbond_it 0.659 r_symmetry_vdw_other 0.348 r_symmetry_vdw_refined 0.292 r_nbd_other 0.27 r_xyhbond_nbd_refined 0.238 r_symmetry_hbond_refined 0.208 r_nbd_refined 0.205 r_nbtor_other 0.113 r_bond_refined_d 0.016 r_gen_planes_other 0.008 r_gen_planes_refined 0.006 r_bond_other_d r_angle_refined_deg r_dihedral_angle_1_deg r_dihedral_angle_2_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other 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_other r_long_range_B_refined 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 7096 Nucleic Acid Atoms Solvent Atoms 302 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing