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Structure of a lamprey variable lymphocyte receptor mutant in complex with a protein antigen
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3G3A PDB ENTRY 3G3A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 8.5 296 8% (w/v) polyethylene glycol 8000, 0.1 M Tris-HCl, pH 8.5, EVAPORATION, temperature 296K
Crystal Properties Matthews coefficient Solvent content 2.76 55.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.874 α = 90 b = 106.244 β = 90 c = 218.544 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 100 CCD ADSC QUANTUM 315 2008-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.0 NSLS X29A
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 2.4 30 0.09 29.1 13.6 60645
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) 2.4 2.48 0.418 6.7 14
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 PDB ENTRY 3G3A 2.4 30 55191 2921 99.86 0.24426 0.24202 0.2431 0.28612 0.2475 RANDOM 44.722
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] -1.92 0.11 1.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.305 r_dihedral_angle_4_deg 20.365 r_dihedral_angle_3_deg 16.741 r_dihedral_angle_1_deg 6.582 r_scangle_it 3.287 r_scbond_it 2.184 r_angle_refined_deg 1.615 r_mcangle_it 1.443 r_mcbond_it 0.835 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.305 r_dihedral_angle_4_deg 20.365 r_dihedral_angle_3_deg 16.741 r_dihedral_angle_1_deg 6.582 r_scangle_it 3.287 r_scbond_it 2.184 r_angle_refined_deg 1.615 r_mcangle_it 1.443 r_mcbond_it 0.835 r_nbtor_refined 0.306 r_nbd_refined 0.221 r_symmetry_vdw_refined 0.186 r_xyhbond_nbd_refined 0.179 r_symmetry_hbond_refined 0.167 r_chiral_restr 0.11 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8291 Nucleic Acid Atoms Solvent Atoms 180 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling