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CRYSTAL STRUCTURE OF HUMAN GERMLINE ANTIBODY IGHV1-69/IGKV3-11
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5I18 5I18,5I19 experimental model PDB 5I19 5I18,5I19
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.1 M MES PH 6.5, 25% PEG 3350, 0.2 M SODIUM FORMATE
Crystal Properties Matthews coefficient Solvent content 2.44 50
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 212.01 α = 90 b = 55.05 β = 97.88 c = 80.29 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 PIXEL DECTRIS PILATUS 6M MIRRORS 2014-02-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.000 APS 17-ID
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 1.9 30 99 0.044 17.8 3.4 71932 -3 33.2
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 1.9 1.95 97.3 0.245 4.7 3.2
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5I18,5I19 1.9 15 70346 1439 98.8 0.19279 0.19223 0.1942 0.22156 0.2243 RANDOM 34.4
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] -1.43 0.11 1.87 -0.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.263 r_dihedral_angle_4_deg 20.218 r_dihedral_angle_3_deg 13 r_long_range_B_refined 7.318 r_dihedral_angle_1_deg 5.724 r_scbond_it 4.672 r_mcangle_it 4.053 r_mcbond_it 3.422 r_angle_refined_deg 1.106 r_chiral_restr 0.068
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.263 r_dihedral_angle_4_deg 20.218 r_dihedral_angle_3_deg 13 r_long_range_B_refined 7.318 r_dihedral_angle_1_deg 5.724 r_scbond_it 4.672 r_mcangle_it 4.053 r_mcbond_it 3.422 r_angle_refined_deg 1.106 r_chiral_restr 0.068 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6425 Nucleic Acid Atoms Solvent Atoms 472 Heterogen Atoms 42
Software Software Software Name Purpose XDS data reduction XDS data scaling PHASER phasing REFMAC refinement