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Crystal structure of MST1 with a MAP4K1 SMOL inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3COM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 295 1.4 M NH4SO4, 0.3 M LiSO4, 0.1 M CAPS pH 9.8
Crystal Properties Matthews coefficient Solvent content 3.09 60.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.447 α = 90 b = 105.627 β = 90 c = 110.563 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 EIGER2 X 16M 2017-04-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.0332 PETRA III, DESY P11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.14 48.98 99.1 0.106 0.998 14.81 7.2 49164 39
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.14 2.27 94.6 0.761 0.813 2.32 6.8
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 2.14 48.98 47064 2100 99.05 0.19591 0.19458 0.2016 0.22581 0.2275 RANDOM 36.335
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] 0.68 -0.38 -0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.988 r_dihedral_angle_4_deg 21.93 r_dihedral_angle_3_deg 15.939 r_dihedral_angle_1_deg 6.658 r_long_range_B_refined 5.161 r_long_range_B_other 5.127 r_scangle_other 3.281 r_mcangle_it 2.284 r_mcangle_other 2.284 r_scbond_it 2.022
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.988 r_dihedral_angle_4_deg 21.93 r_dihedral_angle_3_deg 15.939 r_dihedral_angle_1_deg 6.658 r_long_range_B_refined 5.161 r_long_range_B_other 5.127 r_scangle_other 3.281 r_mcangle_it 2.284 r_mcangle_other 2.284 r_scbond_it 2.022 r_scbond_other 2.021 r_angle_refined_deg 1.602 r_mcbond_it 1.458 r_mcbond_other 1.458 r_angle_other_deg 1.267 r_chiral_restr 0.079 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4423 Nucleic Acid Atoms Solvent Atoms 305 Heterogen Atoms 116
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing Coot model building