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Crystal structure of GFP-LAMA-F98 - a GFP enhancer nanobody with cpDHFR insertion and TMP and NADPH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5UII 5UII, 5H8D experimental model PDB 5H8D 5UII, 5H8D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 0.1 M MES pH 6.0, 30% (v/v) PEG 600, 5% (w/v) PEG 1000, 10% (v/v) glycerol
Crystal Properties Matthews coefficient Solvent content 2.55 51.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.61 α = 90 b = 86.61 β = 90 c = 73.04 γ = 120
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 2018-02-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.97797 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.2 50 99.9 0.058 22.62 10.1 15911
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.3 99.9 0.453 5.32 10.4
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 5UII, 5H8D 2.2 43.305 1.39 15910 796 99.95 0.177 0.1747 0.1772 0.2195 0.2208
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 6.166 f_angle_d 1.068 f_chiral_restr 0.058 f_bond_d 0.008 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2167 Nucleic Acid Atoms Solvent Atoms 52 Heterogen Atoms 79
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing