☰ Navigation Tabs
Crystal structure of a llama VHH antibody BCD090-M2 against human ErbB3 in space group C2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5IMK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293.15 Reservoir solution:
0.1M MES-Imidazole pH 6.5, 0.02M Sodium formate, 0.02M Ammonium acetate, 0.02M Sodium citrate, 0.02M Sodium potassium tartrate, 0.02M Sodium oxamate, 20% v/v PEG 500MME, 10% w/v PEG 20 000
Crystal Properties Matthews coefficient Solvent content 2.13 42.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.759 α = 90 b = 38.931 β = 102.243 c = 47.482 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 CCD APEX II CCD 2017-09-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE BRUKER IMUS MICROFOCUS 1.54184
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 1.59842847381 33.2975053523 98.76472461 0.0731657786164 0.08065 0.0329161383793 0.998 12.7359219637 5.21442847012 15511 9.35381631249
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 1.59842847381 1.62598903761 0.386631506086 2.0696012381 2.29898648649
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5IMK 1.59842847381 33.2975053523 15157 1517 96.5106653932 0.185278623977 0.182239424233 0.1812 0.212561347445 0.209 14.3560089422
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 16.3181533076 f_angle_d 0.822777572893 f_chiral_restr 0.0564492238797 f_bond_d 0.00590462819608 f_plane_restr 0.00507859703921
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 981 Nucleic Acid Atoms Solvent Atoms 190 Heterogen Atoms
Software Software Software Name Purpose APEX 2 data collection SAINT data reduction SADABS data scaling PHASER phasing PHENIX model building Coot model building PHENIX refinement