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Crystal Structure of Nonribosomal peptide synthetases (NRPS), FmoA3 (S1046A)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VSQ 2VSQ, 5T7Z, 5U89, 5ES5 experimental model PDB 5T7Z 2VSQ, 5T7Z, 5U89, 5ES5 experimental model PDB 5U89 2VSQ, 5T7Z, 5U89, 5ES5 experimental model PDB 5ES5 2VSQ, 5T7Z, 5U89, 5ES5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 0.2 M MgCl2, 0.1 M HEPES pH 8.0, and 25%Poly(acrylic acid sodium salt) 5,100
Crystal Properties Matthews coefficient Solvent content 3.45 64.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.355 α = 90 b = 167.65 β = 90 c = 194.12 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RAYONIX MX300-HS 2017-08-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE TPS 05A 1.1000 NSRRC TPS 05A
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 2.45 49.16 100 0.167 0.172 0.044 0.998 14.8 15.2 62173 42.53
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.45 2.51 1.694 0.446 0.746 2.1
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2VSQ, 5T7Z, 5U89, 5ES5 2.45 49.16 1.34 62123 3258 99.98 0.1817 0.1798 0.1822 0.2155 0.2172 46.53
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 7.0577 f_angle_d 0.9048 f_chiral_restr 0.051 f_bond_d 0.008 f_plane_restr 0.0062
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7049 Nucleic Acid Atoms Solvent Atoms 232 Heterogen Atoms 5
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing