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Crystal structure of Indole 3-Carboxylic acid decarboxylase from Arthrobacter nicotianae FI1612 in complex with co-factor prFMN.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7ABO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.1 Carboxylic acid, 0.1 M Buffer System pH 6.5, 30% Precipitant mixture 3
Crystal Properties Matthews coefficient Solvent content 3.17 61.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.2 α = 90 b = 195.45 β = 116.35 c = 105.21 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 80 PIXEL DECTRIS EIGER2 XE 16M 2017-07-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9762 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.53 43.42 98.86 0.994 8.6 3.4 123931
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.53 2.57 0.39
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 7ABO 2.53 43.42 117399 6529 98.79 0.1858 0.1839 0.1893 0.221 0.2242 RANDOM 84.096
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] 0.03 -1.32 3.27 -1.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.026 r_dihedral_angle_4_deg 17.79 r_dihedral_angle_3_deg 17.063 r_dihedral_angle_1_deg 7.23 r_angle_refined_deg 1.701 r_angle_other_deg 1.365 r_chiral_restr 0.074 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.026 r_dihedral_angle_4_deg 17.79 r_dihedral_angle_3_deg 17.063 r_dihedral_angle_1_deg 7.23 r_angle_refined_deg 1.701 r_angle_other_deg 1.365 r_chiral_restr 0.074 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 20763 Nucleic Acid Atoms Solvent Atoms 477 Heterogen Atoms 228
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing PDB_EXTRACT data extraction