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Crystal structure of macaque anti-HIV-1 antibody RM20F
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5CSZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 293 The RM20F Fab was crystallized from
a solution containing 10 mg/mL protein in 1X TBS with a well solution containing 0.1M MES, pH 5.0 and 2M ammonium sulfate. The crystals were cryoprotected by soaking in a well solution
supplemented with 30% ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.82 56.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.459 α = 90 b = 75.646 β = 90 c = 115.068 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 PILATUS 6M 2018-10-10 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) 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 2.176 36.73 98.6 0.84 7.7 4 28053 21.34
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.24 0.54
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5CSZ 2.176 36.721 1.33 27996 1374 97.06 0.1992 0.1972 0.2409 0.2333 28.0592
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 12.346 f_angle_d 0.551 f_chiral_restr 0.044 f_plane_restr 0.003 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3283 Nucleic Acid Atoms Solvent Atoms 288 Heterogen Atoms 20
Software Software Software Name Purpose PHENIX refinement SCALEPACK data scaling PDB_EXTRACT data extraction HKL-2000 data reduction PHASER phasing