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Structure of MAP2K1 complexed with 5Z7-oxozeaenol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5HZE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 8% Tacsimete pH 5.0, 19.5% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.44 49.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.364 α = 90 b = 128.947 β = 94.86 c = 65.689 γ = 90
Symmetry Space Group P 1 21 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 PIXEL DECTRIS EIGER X 16M 2023-06-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.35 47.194 99.6 0.997 10.15 4 32615
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.35 2.49 0.573
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 2.35 45.93 30955 1629 99.59 0.21023 0.20631 0.2152 0.28403 0.2986 RANDOM 94.273
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] -3.47 1.77 -3.69 6.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.884 r_long_range_B_other 15.478 r_long_range_B_refined 15.467 r_mcangle_it 10.652 r_mcangle_other 10.65 r_scangle_other 10.192 r_dihedral_angle_2_deg 7.871 r_mcbond_it 6.903 r_mcbond_other 6.902 r_dihedral_angle_1_deg 6.492
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.884 r_long_range_B_other 15.478 r_long_range_B_refined 15.467 r_mcangle_it 10.652 r_mcangle_other 10.65 r_scangle_other 10.192 r_dihedral_angle_2_deg 7.871 r_mcbond_it 6.903 r_mcbond_other 6.902 r_dihedral_angle_1_deg 6.492 r_scbond_it 6.339 r_scbond_other 6.338 r_angle_refined_deg 1.426 r_angle_other_deg 0.548 r_chiral_restr 0.21 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 4832 Nucleic Acid Atoms Solvent Atoms 137 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing