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Crystal structure of MAPKAPK2 (MK2) complexed with PF-3644022 and 5-(4-bromophenyl)-N-[4-(1-piperazinyl)phenyl]-N-(2-pyridinylmethyl)-2-furancarboxamide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NY3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 295 1.3M NaMalonate, 0.1M Hepes pH6.0, 0.5% jeffamine ED2003
Crystal Properties Matthews coefficient Solvent content 3.39 63.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.531 α = 90 b = 287.339 β = 90 c = 148.407 γ = 90
Symmetry Space Group C 2 2 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 PILATUS3 6M 2013-09-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97625 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.81 143.67 100 0.083 0.1 0.998 10.6 6.1 68678
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.81 2.88 99.7 1.495 0.668 1 6.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 1NY3 2.81 120 68521 3441 99.8 0.2287 0.2277 0.2296 0.2472 0.2437 RANDOM 92.85
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] -31.8877 26.9223 4.9654
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.84 t_omega_torsion 2.72 t_angle_deg 0.96 t_bond_d 0.008 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.84 t_omega_torsion 2.72 t_angle_deg 0.96 t_bond_d 0.008 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13480 Nucleic Acid Atoms Solvent Atoms 35 Heterogen Atoms 372
Software Software Software Name Purpose BUSTER refinement xia2 data reduction PDB_EXTRACT data extraction DIALS data scaling PHASER phasing