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X-ray structure of the human mitogen-activated protein kinase kinase 1 (MEK1) in complex with an inhibitor and MgATP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1S9J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.8 279 PEG 4000, pH 8.8, VAPOR DIFFUSION, HANGING DROP, temperature 279K
Crystal Properties Matthews coefficient Solvent content 2.27 45.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.894 α = 90 b = 129.09 β = 90 c = 135.736 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 95 CCD ADSC QUANTUM 315 2005-11-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.000 Photon Factory BL-5A
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 50 96.9 71391 69248 1 1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 1S9J 2 20 71391 63327 3323 94.18 0.19938 0.19799 0.22531 0.2242 RANDOM 40.549
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] 0.53 -0.1 -0.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.918 r_dihedral_angle_4_deg 20.376 r_dihedral_angle_3_deg 13.754 r_dihedral_angle_1_deg 5.552 r_angle_refined_deg 1.26 r_chiral_restr 0.082 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.918 r_dihedral_angle_4_deg 20.376 r_dihedral_angle_3_deg 13.754 r_dihedral_angle_1_deg 5.552 r_angle_refined_deg 1.26 r_chiral_restr 0.082 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_it r_mcbond_other r_mcangle_it r_scbond_it 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 6731 Nucleic Acid Atoms Solvent Atoms 230 Heterogen Atoms 174
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling