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Crystal structure of M2 PYK in complex with Serine.
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 2.26 45.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.35 α = 89.72 b = 108.94 β = 71.13 c = 124.34 γ = 66.94
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 2014-08-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.97624 Diamond I24
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 2.96 116.5 98.6 8.4 2.7 88052
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 2.96 3.04
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 4fxj 2.96 116.5 82638 4203 98.63 0.23677 0.23603 0.233 0.25159 0.2465 RANDOM 93.425
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] -0.45 0.27 0.3 0.91 0.34 -0.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.316 r_dihedral_angle_3_deg 15.413 r_dihedral_angle_4_deg 14.052 r_long_range_B_refined 5.363 r_long_range_B_other 5.363 r_dihedral_angle_1_deg 5.329 r_mcangle_it 3.577 r_mcangle_other 3.577 r_scangle_other 2.712 r_mcbond_it 2.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.316 r_dihedral_angle_3_deg 15.413 r_dihedral_angle_4_deg 14.052 r_long_range_B_refined 5.363 r_long_range_B_other 5.363 r_dihedral_angle_1_deg 5.329 r_mcangle_it 3.577 r_mcangle_other 3.577 r_scangle_other 2.712 r_mcbond_it 2.003 r_mcbond_other 2.003 r_scbond_it 1.471 r_scbond_other 1.471 r_angle_refined_deg 1.163 r_angle_other_deg 0.887 r_chiral_restr 0.062 r_bond_refined_d 0.008 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 31232 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 112
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing