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CRYSTAL STRUCTURE OF HUMAN GERMLINE ANTIBODY IGHV3-23/IGKV4-1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2B2X 2B2X,1LVE experimental model PDB 1LVE 2B2X,1LVE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 2.0 M AMMONIUM SULFATE, 2% PEG 400, 0.1 M HEPES PH 7.5
Crystal Properties Matthews coefficient Solvent content 2.87 57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.71 α = 90 b = 111 β = 90 c = 159.99 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 95 CCD RIGAKU SATURN 944 VARIMAX HF 2008-04-23 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 30 99.7 0.094 21.6 11.6 75540 -3 29.4
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 2.06 96.9 0.488 5 9.2
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2B2X,1LVE 2 15 74238 1109 98.2 0.21632 0.21578 0.25132 0.2249 RANDOM 46.4
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] 0.94 -0.23 -0.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.345 r_scangle_it 24.83 r_dihedral_angle_4_deg 23.87 r_scbond_it 23.763 r_dihedral_angle_3_deg 13.55 r_dihedral_angle_1_deg 5.897 r_mcangle_it 4.752 r_mcbond_it 2.812 r_angle_refined_deg 1.148 r_chiral_restr 0.071
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.345 r_scangle_it 24.83 r_dihedral_angle_4_deg 23.87 r_scbond_it 23.763 r_dihedral_angle_3_deg 13.55 r_dihedral_angle_1_deg 5.897 r_mcangle_it 4.752 r_mcbond_it 2.812 r_angle_refined_deg 1.148 r_chiral_restr 0.071 r_bond_refined_d 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_refined 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_other r_long_range_B_refined 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 6548 Nucleic Acid Atoms Solvent Atoms 635 Heterogen Atoms 15
Software Software Software Name Purpose XDS data reduction XDS data scaling PHASER phasing REFMAC refinement