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Crystal Structure of Mnk2-D228G in complex with Staurosporine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2AC3 PDB ENTRY 2AC3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.6 293 Polyacrylic acid, pH 7.6, VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.25 62.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.366 α = 90 b = 102.366 β = 90 c = 76.439 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 100 IMAGE PLATE MAR scanner 345 mm plate 2005-08-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.98008 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.7 30 99.7 5.8 12900 12862 2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2AC3 2.71 30 2 12254 12218 627 99.69 0.2034 0.20131 0.24566 0.2658 RANDOM 69.244
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] -0.98 -0.49 -0.98 1.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.284 r_dihedral_angle_3_deg 19.725 r_dihedral_angle_4_deg 16.266 r_dihedral_angle_1_deg 6.497 r_scangle_it 2.15 r_angle_refined_deg 1.389 r_scbond_it 1.208 r_mcangle_it 1.13 r_mcbond_it 0.615 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.284 r_dihedral_angle_3_deg 19.725 r_dihedral_angle_4_deg 16.266 r_dihedral_angle_1_deg 6.497 r_scangle_it 2.15 r_angle_refined_deg 1.389 r_scbond_it 1.208 r_mcangle_it 1.13 r_mcbond_it 0.615 r_nbtor_refined 0.307 r_symmetry_vdw_refined 0.225 r_nbd_refined 0.222 r_symmetry_hbond_refined 0.179 r_xyhbond_nbd_refined 0.149 r_chiral_restr 0.098 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2163 Nucleic Acid Atoms Solvent Atoms 21 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing