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CRYSTAL STRUCTURE OF HUMAN GERMLINE ANTIBODY IGHV3-23/IGKV3-20
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5I1D 5I1D,1DN0 experimental model PDB 1DN0 5I1D,1DN0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 16% PEG 3K, 0.2 M AMMONIUM ACETATE, 0.1 M MES PH 6.5
Crystal Properties Matthews coefficient Solvent content 3.6 66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.46 α = 90 b = 121.46 β = 90 c = 160.39 γ = 120
Symmetry Space Group P 62 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 CCD RIGAKU SATURN 944 VARIMAX HF 2008-10-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
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 2.25 30 96.9 0.086 37 27.2 32572 -3 33.7
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 2.25 2.31 94.8 0.478 10.4 26.1
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 5I1D,1DN0 2.25 15 31411 1029 96.5 0.22147 0.22003 0.2268 0.2663 0.2728 RANDOM 47.7
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] 0.8 0.4 0.8 -2.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.36 r_dihedral_angle_4_deg 21.565 r_dihedral_angle_3_deg 12.891 r_long_range_B_refined 8.683 r_scbond_it 5.931 r_dihedral_angle_1_deg 5.888 r_mcangle_it 5.792 r_mcbond_it 4.472 r_angle_refined_deg 1.055 r_chiral_restr 0.062
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.36 r_dihedral_angle_4_deg 21.565 r_dihedral_angle_3_deg 12.891 r_long_range_B_refined 8.683 r_scbond_it 5.931 r_dihedral_angle_1_deg 5.888 r_mcangle_it 5.792 r_mcbond_it 4.472 r_angle_refined_deg 1.055 r_chiral_restr 0.062 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 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 3237 Nucleic Acid Atoms Solvent Atoms 222 Heterogen Atoms 13
Software Software Software Name Purpose XDS data reduction XDS data scaling PHASER phasing REFMAC refinement