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Crystal structure of an anti-idiotype VLR
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3TWI 3TWI, modified
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 277 0.1M Tris pH8.5
0.2M magnesium chloride
24%(w/v) peg-4000
Crystal Properties Matthews coefficient Solvent content 2.08 40.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.415 α = 110.09 b = 61.382 β = 99.79 c = 80.562 γ = 93.52
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 PILATUS 6M 2017-03-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.97946 SSRL BL12-2
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 1.498 34.72 85.1 0.06423 0.07523 0.03892 0.997 11.05 3.7 145338 19.33
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 1.498 1.552 52.73 0.7363 0.8594 0.4409 0.732 1.49 3.7
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3TWI, modified 1.498 34.72 145247 7053 85.1 0.1949 0.1934 0.2234 0.2375
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 15.054 f_angle_d 0.871 f_chiral_restr 0.077 f_bond_d 0.006 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8665 Nucleic Acid Atoms Solvent Atoms 943 Heterogen Atoms 4
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHENIX phasing