☰ Navigation Tabs
Crystal structure of HL4E10 Fab, a hamster Ab stimulatory for gammadelta T cells
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1W72 HL4E10 LIGHT CHAIN SEQUENCE THREADED ONTO 1W72, HL4E10 HEAVY CHAIN SEQUENCE THREADED ONTO 2ARJ experimental model PDB 2ARJ HL4E10 LIGHT CHAIN SEQUENCE THREADED ONTO 1W72, HL4E10 HEAVY CHAIN SEQUENCE THREADED ONTO 2ARJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 295 10-12.5 % PEG 4000, 0.1 M NA- ACETATE, 0.2 M (NH4)2SO4, pH 4.60, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.32 46.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.836 α = 90 b = 148.768 β = 106.23 c = 68.798 γ = 90
Symmetry Space Group P 1 21 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 325 mm CCD FLAT MIRROR (VERTICAL FOCUSING), SINGLE CRYSTAL SI(111) BENT MONOCHROMATOR (HORIZONTAL FOCUSING) 2006-07-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 SSRL BL11-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.94 30 95.3 0.105 0.105 7.7 2.3 17012 70.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.94 3.06 96.1 0.541 0.541 1.7
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 HL4E10 LIGHT CHAIN SEQUENCE THREADED ONTO 1W72, HL4E10 HEAVY CHAIN SEQUENCE THREADED ONTO 2ARJ 2.94 30 16120 863 94.5 0.23 0.227 0.2307 0.281 0.2866 RANDOM 54.67
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] 4.15 -2.78 -1.05 -4.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.775 r_dihedral_angle_3_deg 14.298 r_dihedral_angle_4_deg 10.274 r_dihedral_angle_1_deg 5.766 r_angle_refined_deg 0.957 r_angle_other_deg 0.744 r_scangle_it 0.395 r_scbond_it 0.259 r_mcangle_it 0.184 r_nbd_refined 0.178
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.775 r_dihedral_angle_3_deg 14.298 r_dihedral_angle_4_deg 10.274 r_dihedral_angle_1_deg 5.766 r_angle_refined_deg 0.957 r_angle_other_deg 0.744 r_scangle_it 0.395 r_scbond_it 0.259 r_mcangle_it 0.184 r_nbd_refined 0.178 r_nbtor_refined 0.173 r_nbd_other 0.171 r_mcbond_it 0.148 r_symmetry_hbond_refined 0.133 r_symmetry_vdw_other 0.131 r_xyhbond_nbd_refined 0.129 r_symmetry_vdw_refined 0.125 r_nbtor_other 0.079 r_chiral_restr 0.056 r_mcbond_other 0.021 r_bond_refined_d 0.006 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6320 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling