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NpsA-ThdA, an artificially fused Adenylation-PCP di-domain NRPS from Klebsiella oxytoca
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6VHU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 287 protein solution (19 mg/mL): 10 mM HEPES pH 8.0, 25 mM NaCl, 0.4 mM TCEP, 2.5 mM MgCl2, 5% v/v glycerol, 1.2 mM 3-hydroxybenzoyl-AVS, well solution: (0.2 M sodium formate, 20% w/v PEG3350, microbatch drop: 1.2 uL protein solution, 1 uL well solution (under paraffin oil)
Crystal Properties Matthews coefficient Solvent content 2.53 51.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.54 α = 95.331 b = 98.721 β = 96.337 c = 118.754 γ = 106.508
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2019-04-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.97946 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 3 93.84 90.9 0.116 0.124 0.045 0.997 12.2 7.6 45795 74.91
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3 3.05 87.7 0.882 0.945 0.338 0.742 2.3 7.7
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 6vhu 3 47.61 2 45767 2238 90.84 0.2163 0.2141 0.2171 0.2604 0.2627 83.62
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 14.3123 f_angle_d 0.731 f_chiral_restr 0.0519 f_bond_d 0.006 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15234 Nucleic Acid Atoms Solvent Atoms 1 Heterogen Atoms 201
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling autoPROC data scaling PHASER phasing Coot model building