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Chikungunya virus neutralizing antibody 9.8B Fab fragment
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DGG PDB ENTRY 3DGG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 298 25% PEG 3350, 0.1M Tris-Cl pH 8.5 and 0.2M lithium sulfate., VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.18 61.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.859 α = 90 b = 57.726 β = 97.51 c = 118.108 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 MARMOSAIC 300 mm CCD mirrors 2010-10-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 0.96801 APS 23-ID-B
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 2.995 50 99.6 0.095 22.5 3.6 11921 11714 62.7
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 2.995 3.05 98 0.388 4.3 3.4 590
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 THROUGHOUT PDB ENTRY 3DGG 2.995 43.42 11921 11349 568 99.03 0.3251 0.3251 0.32334 0.3138 0.3593 0.353 RANDOM 82.987
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] -1.3 -1.72 2.05 -1.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.398 r_dihedral_angle_3_deg 14.516 r_dihedral_angle_4_deg 10.535 r_dihedral_angle_1_deg 3.944 r_angle_refined_deg 0.91 r_nbtor_refined 0.288 r_symmetry_vdw_refined 0.212 r_scangle_it 0.181 r_nbd_refined 0.166 r_scbond_it 0.108
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.398 r_dihedral_angle_3_deg 14.516 r_dihedral_angle_4_deg 10.535 r_dihedral_angle_1_deg 3.944 r_angle_refined_deg 0.91 r_nbtor_refined 0.288 r_symmetry_vdw_refined 0.212 r_scangle_it 0.181 r_nbd_refined 0.166 r_scbond_it 0.108 r_mcangle_it 0.106 r_xyhbond_nbd_refined 0.088 r_chiral_restr 0.062 r_mcbond_it 0.059 r_symmetry_hbond_refined 0.028 r_bond_refined_d 0.006 r_gen_planes_refined 0.002 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3280 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling