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Crystal structure of human MAP4K1 with an inhibitor, BAY-405
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other previously solved structure
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 0.1M TRIS pH 8.0, 20 % MPD
Crystal Properties Matthews coefficient Solvent content 2.21 44.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.723 α = 90 b = 100.205 β = 90 c = 39.497 γ = 90
Symmetry Space Group P 21 21 2
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 PILATUS3 S 6M 2020-03-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9184 BESSY 14.1
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 41.95 98.6 0.113 0.999 14.22 7.2 20999
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 2.12 97.7 1.694 0.703 1.29 7.1
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 41.95 19949 1050 98.55 0.24221 0.23953 0.2483 0.29244 0.2956 RANDOM 56.109
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] -1.22 -2.41 3.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.927 r_dihedral_angle_4_deg 22.935 r_dihedral_angle_3_deg 18.235 r_dihedral_angle_1_deg 6.954 r_long_range_B_refined 6.598 r_long_range_B_other 6.583 r_mcangle_it 4.156 r_mcangle_other 4.155 r_scangle_other 3.948 r_mcbond_it 2.589
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.927 r_dihedral_angle_4_deg 22.935 r_dihedral_angle_3_deg 18.235 r_dihedral_angle_1_deg 6.954 r_long_range_B_refined 6.598 r_long_range_B_other 6.583 r_mcangle_it 4.156 r_mcangle_other 4.155 r_scangle_other 3.948 r_mcbond_it 2.589 r_mcbond_other 2.588 r_scbond_it 2.438 r_scbond_other 2.437 r_angle_refined_deg 1.519 r_angle_other_deg 1.208 r_chiral_restr 0.071 r_bond_refined_d 0.007 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 2125 Nucleic Acid Atoms Solvent Atoms 47 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing Coot model building