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Crystal structure of M2 PYK in complex with Phenyalanine.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4FXJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 290 10-16% PEG 3350, 100 mM sodium Cacodylate, 50 mM MgCl2, 100 mM KCl,
Crystal Properties Matthews coefficient Solvent content 2.3 46.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.37 α = 90 b = 70.34 β = 106.06 c = 168.64 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 PILATUS 6M-F 2014-12-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9174 Diamond I04-1
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 2.46 162.1 98.8 14.2 5.8 80146
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.46 2.524
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4fxj 2.46 162.06 75137 3904 98.62 0.19808 0.19665 0.22463 0.2107 RANDOM 63.614
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] 1.23 1 -1.35 -0.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.893 r_dihedral_angle_4_deg 16.768 r_dihedral_angle_3_deg 13.615 r_long_range_B_refined 5.361 r_long_range_B_other 5.347 r_dihedral_angle_1_deg 5.302 r_scangle_other 3.362 r_mcangle_it 3.214 r_mcangle_other 3.214 r_scbond_it 1.975
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.893 r_dihedral_angle_4_deg 16.768 r_dihedral_angle_3_deg 13.615 r_long_range_B_refined 5.361 r_long_range_B_other 5.347 r_dihedral_angle_1_deg 5.302 r_scangle_other 3.362 r_mcangle_it 3.214 r_mcangle_other 3.214 r_scbond_it 1.975 r_scbond_other 1.975 r_mcbond_it 1.892 r_mcbond_other 1.892 r_angle_refined_deg 1.272 r_angle_other_deg 0.898 r_chiral_restr 0.068 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 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 14102 Nucleic Acid Atoms Solvent Atoms 353 Heterogen Atoms 92
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing