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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 3.06 59.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.31 α = 90 b = 104.966 β = 90 c = 110.188 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 1.9 48.78 94.5 0.051 1 23.89 6.5 66175 35.8
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 1.9 2.01 71.4 0.523 0.846 2.5 3.9
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 1.9 48.78 64075 2100 94.5 0.17717 0.17604 0.1844 0.21238 0.2153 RANDOM 35.126
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] 1.18 0.01 -1.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.093 r_dihedral_angle_4_deg 24.16 r_dihedral_angle_3_deg 14.879 r_dihedral_angle_1_deg 6.408 r_long_range_B_refined 6.119 r_long_range_B_other 5.938 r_scangle_other 3.414 r_mcangle_it 2.3 r_mcangle_other 2.299 r_scbond_it 2.143
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.093 r_dihedral_angle_4_deg 24.16 r_dihedral_angle_3_deg 14.879 r_dihedral_angle_1_deg 6.408 r_long_range_B_refined 6.119 r_long_range_B_other 5.938 r_scangle_other 3.414 r_mcangle_it 2.3 r_mcangle_other 2.299 r_scbond_it 2.143 r_scbond_other 2.142 r_angle_refined_deg 1.551 r_mcbond_it 1.478 r_mcbond_other 1.478 r_angle_other_deg 1.315 r_chiral_restr 0.075 r_bond_refined_d 0.008 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 4417 Nucleic Acid Atoms Solvent Atoms 519 Heterogen Atoms 88
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing Coot model building