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K245A mutant of L-tyrosine decarboxylase from Methanocaldococcus jannaschii complexed with a post-decarboxylation quinonoid-like intermediate formed with L-tyrosine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6LDR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.4 293 0.1M sodium citrate pH 5.4, 0.2M sodium potassium tartarate, 2.0M ammonium sulphate
Crystal Properties Matthews coefficient Solvent content 3.3 62.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.37 α = 90 b = 98.37 β = 90 c = 121.72 γ = 90
Symmetry Space Group P 43 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 IMAGE PLATE MARRESEARCH 2015-03-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 1.93 38.25 100 0.129 0.134 0.037 0.998 14.1 13 45548 25.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.93 1.98 99.8 1.142 1.193 0.342 0.716 2.3 11.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 6LDR 1.93 38.25 1.33 45424 2229 99.84 0.1898 0.1879 0.1882 0.2266 0.2272 RANDOM 27.8448
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.268 f_angle_d 0.764 f_chiral_restr 0.055 f_bond_d 0.006 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2922 Nucleic Acid Atoms Solvent Atoms 273 Heterogen Atoms 48
Software Software Software Name Purpose PHENIX refinement Aimless data scaling PDB_EXTRACT data extraction iMOSFLM data reduction PHENIX phasing