☰ Navigation Tabs
Llama nanobody nb18 raised against GldL from Flavobacterium jonhsoniae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1T2J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 293 100mM sodium acetate pH 4.5, 200mM calcium acetate, 30% PEG 400
Crystal Properties Matthews coefficient Solvent content 2.75 55.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.857 α = 90 b = 95.857 β = 90 c = 118.895 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 EIGER X 16M 2018-01-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.978 SOLEIL PROXIMA 1
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 2.59 44.45 99.8 0.994 9 6.5 19199
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 2.59 2.75 0.46
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 1T2J 2.59 44.45 18270 926 99.83 0.1951 0.1927 0.1943 0.2427 0.2385 RANDOM 73.144
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] 1.5 1.5 -3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.966 r_dihedral_angle_4_deg 21.299 r_dihedral_angle_3_deg 18.998 r_dihedral_angle_1_deg 8.127 r_angle_refined_deg 1.778 r_angle_other_deg 1.278 r_chiral_restr 0.072 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.966 r_dihedral_angle_4_deg 21.299 r_dihedral_angle_3_deg 18.998 r_dihedral_angle_1_deg 8.127 r_angle_refined_deg 1.778 r_angle_other_deg 1.278 r_chiral_restr 0.072 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3633 Nucleic Acid Atoms Solvent Atoms 276 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling MOLREP phasing