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Tryptophan synthase Q114A mutant in complex with inhibitor N-(4'-trifluoromethoxybenzenesulfonyl)-2-amino-1-ethylphosphate (F9F) at the alpha-site, aminoacrylate at the beta site, and cesium ion at the metal coordination site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2CLL PDB entry 2CLL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.8 298 50 mM bicine-CsOH, 8-10% PEG8000, 2-6 mM spermine, 1 mM DTT
Crystal Properties Matthews coefficient Solvent content 2.63 53.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 183.73 α = 90 b = 60.88 β = 94.87 c = 67.32 γ = 90
Symmetry Space Group C 1 2 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 IMAGE PLATE RIGAKU RAXIS IV++ VariMax HF 2017-11-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 1.64 91.533 90 0.056 0.079 0.041 10.5 3.6 81464 81464
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.64 1.73 83.6 0.213 0.213 0.296 0.152 3.1 3.6
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 PDB entry 2CLL 1.64 37.32 77328 4044 89.57 0.1318 0.1295 0.1303 0.175 0.1759 RANDOM 21.925
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] -0.73 0.22 1.72 -1.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.339 r_sphericity_free 22.944 r_dihedral_angle_4_deg 16.807 r_dihedral_angle_3_deg 12.006 r_sphericity_bonded 10.634 r_dihedral_angle_1_deg 6.288 r_rigid_bond_restr 2.395 r_angle_refined_deg 1.516 r_chiral_restr 0.103 r_bond_refined_d 0.009
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.339 r_sphericity_free 22.944 r_dihedral_angle_4_deg 16.807 r_dihedral_angle_3_deg 12.006 r_sphericity_bonded 10.634 r_dihedral_angle_1_deg 6.288 r_rigid_bond_restr 2.395 r_angle_refined_deg 1.516 r_chiral_restr 0.103 r_bond_refined_d 0.009 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4996 Nucleic Acid Atoms Solvent Atoms 794 Heterogen Atoms 169
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing DM phasing PDB_EXTRACT data extraction