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COMPLEX OF A DROMEDARY SINGLE-DOMAIN VHH ANTIBODY FRAGMENT WITH RNASE A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RUV PDB ENTRY 1RUV AND PDB ENTRY 1MEL experimental model PDB 1MEL PDB ENTRY 1RUV AND PDB ENTRY 1MEL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.4 HANGING DROP METHOD. 5 MG/ML OF THE COMPLEX RESERVOIR SOLUTION IS 0.1 M POTASSIUM PHOSPHATE PH 6.4 15 TO 20% W/V PEG 8000, vapor diffusion - hanging drop
Crystal Properties Matthews coefficient Solvent content 2.11 50.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.52 α = 91.43 b = 66.82 β = 117.34 c = 69.34 γ = 97.33
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 293 IMAGE PLATE MARRESEARCH M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.8 15 99.2 0.111 8.5 3.8 25413
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.8 2.9 98.2 0.336 3.9 3.9
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1RUV AND PDB ENTRY 1MEL 2.8 20 25796 1298 98.5 0.22234 0.1965 0.28244 0.2472 RANDOM 27.26
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 p_staggered_tor 25.9 p_transverse_tor 25.8 p_planar_tor 3.2 p_mcangle_it 1.524 p_scangle_it 1.39 p_mcbond_it 0.833 p_scbond_it 0.81 p_multtor_nbd 0.235 p_singtor_nbd 0.183 p_xyhbond_nbd 0.183
RMS Deviations Key Refinement Restraint Deviation p_staggered_tor 25.9 p_transverse_tor 25.8 p_planar_tor 3.2 p_mcangle_it 1.524 p_scangle_it 1.39 p_mcbond_it 0.833 p_scbond_it 0.81 p_multtor_nbd 0.235 p_singtor_nbd 0.183 p_xyhbond_nbd 0.183 p_chiral_restr 0.094 p_angle_d 0.026 p_planar_d 0.021 p_bond_d 0.007 p_angle_deg p_hb_or_metal_coord p_plane_restr p_xhyhbond_nbd p_orthonormal_tor p_special_tor
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7544 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 20
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling AMoRE phasing REFMAC refinement