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Crystal structure for the FnIII module of mouse LEP-R in complex with the anti-LEP-R nanobody VHH-4.80
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OHQ 1OHQ, AF-P48356-F1-model_v1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 293 0.2 M ammonium sulphate
0.1 M Na cacodylate pH 5.6
30% PEG Smear Medium
Crystal Properties Matthews coefficient Solvent content 2.15 42.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.192 α = 90 b = 85.876 β = 90 c = 144.689 γ = 90
Symmetry Space Group P 21 21 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 PIXEL DECTRIS EIGER X 16M adaptive KB-mirrors 2022-05-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.972418 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 1.75 90 100 0.164 0.998 10.48 11.9 67680 -3 32.147
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.86 99.9 2.066 0.326 0.86 11.5
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 1OHQ, AF-P48356-F1-model_v1 1.75 25.42 67651 3373 100 0.1953 0.1934 0.191 0.2333 0.2283 RANDOM 38.46
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] 1.6091 -2.2495 0.6404
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 15.69 t_omega_torsion 3.71 t_angle_deg 0.93 t_bond_d 0.008 t_dihedral_angle_d t_gen_planes t_it t_chiral_improper_torsion t_sum_occupancies t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5131 Nucleic Acid Atoms Solvent Atoms 514 Heterogen Atoms 106
Software Software Software Name Purpose BUSTER refinement XDS data reduction Aimless data scaling PHASER phasing