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Crystal Structure of the GRAM-4 antibody fragment in complex with NAGG peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5X0T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 289 Protein buffer: 8 mg/ml in 10 mM HEPES, pH 7, 150 mM NaCl, 2 mM EDTA. Crystallization: G5 Morpheus. 0.1 M Carboxylic acids; 0.1 M Buffer system 2; 30% Precipitant Mix 1. 10% w/v PEG 20000, 20% v/v PEG MME 550, 0.1M MOPS/HEPES-Na pH7.5, 0.02 M sodium formate, 0.02M ammonium acetate, 0.02M trisodium citrate, 0.02M sodium potassium L-tartrate, 0.02M sodium oxamate
Crystal Properties Matthews coefficient Solvent content 2.49 50.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 177.73 α = 90 b = 40 β = 100.996 c = 71.41 γ = 90
Symmetry Space Group C 1 2 1
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 9M NSLSII AMX BEAMLINE BL17-ID 2025-03-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON OTHER 0.920194
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 2.65 35 99.9 0.232 0.251 0.095 0.986 14.3 6.9 14696 34.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.65 2.74 99.7 0.903 0.986 0.391 0.057 1.7 6.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.65 34.71 1.36 14689 732 99.91 0.2199 0.2184 0.2184 0.2473 0.247 Random selection 43.87
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 5.4345 f_angle_d 0.5721 f_chiral_restr 0.0443 f_plane_restr 0.0071 f_bond_d 0.0022
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3345 Nucleic Acid Atoms Solvent Atoms 104 Heterogen Atoms 6
Software Software Software Name Purpose PHENIX refinement XDS data scaling XDS data reduction PHASER phasing PDB_EXTRACT data extraction