☰ Navigation Tabs
Crystal structure of the Fab fragment of the human neutralizing anti-West Nile Virus MAb CR4354
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3KYK WAM homology model of variable domain + constant domain of PDB ID 3KYK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 reservoir solution: 20% PEG8000, 10mM MES buffer, pH6.0, 200mM Ca(OAc)2, starting protein concentration in drop: 8 mg/ml, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.42 49.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.741 α = 90 b = 71.068 β = 90 c = 118.597 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 CCD MARMOSAIC 300 mm CCD 300x300mm2 active area, ~2.2sec read-time, 4096x4096 of 0.072mm pixels 2010-04-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.0332 APS 23-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.43 50 90.8 0.072 13.6 6.7 78075 78075
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) 1.43 1.45 39.4 0.542 1.63 2.7 1674
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 WAM homology model of variable domain + constant domain of PDB ID 3KYK 1.434 45.531 1.34 78002 77999 3868 91.3 0.168 0.167 0.1626 0.186 0.1808 RANDOM 19.731
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] 1.441 0.771 -2.211
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16.384 f_angle_d 1.128 f_chiral_restr 0.073 f_bond_d 0.006 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3349 Nucleic Acid Atoms Solvent Atoms 821 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction HKL-2000 data collection