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Crystal structure of Phenazine 1-carboxylic acid decarboxylase from Mycobacterium fortuitum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7ABN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.06 M Divalents, 0.1 M Buffer System 2 pH 7.5, 30% Precipitant mix 3
Crystal Properties Matthews coefficient Solvent content 2.94 58.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 124.696 α = 90 b = 124.696 β = 90 c = 68.846 γ = 120
Symmetry Space Group P 3 1 2
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 2019-03-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 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 2.35 58.42 100 1 16.6 10.4 25728
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 2.35 2.39 0.6
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 7ABN 2.65 58.12 16994 866 99.83 0.1881 0.1844 0.1844 0.2581 0.2583 RANDOM 71.789
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] -0.54 -0.27 -0.54 1.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.155 r_dihedral_angle_3_deg 20.276 r_dihedral_angle_4_deg 19.478 r_dihedral_angle_1_deg 8.53 r_angle_refined_deg 2.01 r_chiral_restr 0.137 r_bond_refined_d 0.01 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3663 Nucleic Acid Atoms Solvent Atoms 44 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction xia2 data reduction XDS data scaling PHASER phasing