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CRYSTAL STRUCTURE OF HUMAN GERMLINE ANTIBODY IGHV3-53/IGKV4-1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5I1D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.1 M MES PH 6.5, 17% PEG 3K, 0.2 M SODIUM FORMATE, 5% MPD
Crystal Properties Matthews coefficient Solvent content 2.64 53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.05 α = 90 b = 68.05 β = 90 c = 95.59 γ = 120
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 2008-11-24 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 2.5 30 98.6 0.047 31.6 8.2 16727 -3 54.8
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 2.5 2.57 98.1 0.445 5.6 8.1
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 2.5 15 15811 844 98.3 0.25425 0.25012 0.2563 0.33698 0.3436 RANDOM 88.9
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] 1.13 0.56 1.13 -3.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.441 r_dihedral_angle_4_deg 18.187 r_dihedral_angle_3_deg 17.2 r_long_range_B_refined 13.435 r_mcangle_it 10.02 r_mcbond_it 6.547 r_scbond_it 6.438 r_dihedral_angle_1_deg 5.808 r_angle_refined_deg 1.144 r_chiral_restr 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.441 r_dihedral_angle_4_deg 18.187 r_dihedral_angle_3_deg 17.2 r_long_range_B_refined 13.435 r_mcangle_it 10.02 r_mcbond_it 6.547 r_scbond_it 6.438 r_dihedral_angle_1_deg 5.808 r_angle_refined_deg 1.144 r_chiral_restr 0.07 r_bond_refined_d 0.006 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 3218 Nucleic Acid Atoms Solvent Atoms 21 Heterogen Atoms
Software Software Software Name Purpose XDS data reduction XDS data scaling PHASER phasing REFMAC refinement