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MAP4K4 in complex with a pyridin-2(1H)-one derivative
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4U43 PDB Entry 4U43
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.4 293 0.1M MES, 14% v/v PEG 8000, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.19 43.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.99 α = 90 b = 90.25 β = 90 c = 90.97 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 90 PIXEL PSI PILATUS 6M Dynamic bendable mirror 2014-05-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.007180 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.4 45.49 99.9 0.089 16.64 6.47 26397 26382 -3 58.827
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.46 100 0.012 1.79 6.8 1926
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB Entry 4U43 2.4 45.49 26397 26382 1319 99.93 0.2121 0.2087 0.2132 0.2776 0.281 RANDOM 54.233
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] -0.98 1.26 -0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.148 r_dihedral_angle_4_deg 18.453 r_dihedral_angle_3_deg 17.998 r_dihedral_angle_1_deg 5.872 r_mcangle_it 4.121 r_scbond_it 2.87 r_mcbond_it 2.561 r_angle_refined_deg 1.225 r_chiral_restr 0.091 r_bond_refined_d 0.007
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.148 r_dihedral_angle_4_deg 18.453 r_dihedral_angle_3_deg 17.998 r_dihedral_angle_1_deg 5.872 r_mcangle_it 4.121 r_scbond_it 2.87 r_mcbond_it 2.561 r_angle_refined_deg 1.225 r_chiral_restr 0.091 r_bond_refined_d 0.007 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4585 Nucleic Acid Atoms Solvent Atoms 76 Heterogen Atoms 34
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data scaling