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Crystal structure of LkcE R326Q mutant in complex with its substrate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6F32
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 16% PEG 8000, 160 mM calcium acetate, 100 mM Bis Tris pH 6.5
Crystal Properties Matthews coefficient Solvent content 3.13 60.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 125.554 α = 90 b = 125.554 β = 90 c = 156.655 γ = 90
Symmetry Space Group P 41 21 2
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 2016-02-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.97857 SOLEIL PROXIMA 1
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 2.5 48.99 99.6 0.047 0.053 0.999 20.24 4.406 43788 63.373
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.6 99.4 0.635 0.72 0.751 2.42 4.403
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 6F32 2.5 48.99 41613 2191 99.42 0.2075 0.2056 0.2049 0.2438 0.2431 RANDOM 61.342
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] 0.81 0.81 -1.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.924 r_dihedral_angle_4_deg 18.423 r_dihedral_angle_3_deg 16.035 r_dihedral_angle_1_deg 4.556 r_angle_refined_deg 1.79 r_angle_other_deg 1.479 r_chiral_restr 0.102 r_bond_refined_d 0.015 r_bond_other_d 0.009 r_gen_planes_refined 0.009
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.924 r_dihedral_angle_4_deg 18.423 r_dihedral_angle_3_deg 16.035 r_dihedral_angle_1_deg 4.556 r_angle_refined_deg 1.79 r_angle_other_deg 1.479 r_chiral_restr 0.102 r_bond_refined_d 0.015 r_bond_other_d 0.009 r_gen_planes_refined 0.009 r_gen_planes_other 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6782 Nucleic Acid Atoms Solvent Atoms 230 Heterogen Atoms 235
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction Coot model building