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AL-09 H87Y, immunoglobulin light chain variable domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Q20
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.3 295 30% w/v polyethylene glycol 4000 and 0.2 M Li2SO4 in 0.1 M Tris buffer, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 3.15 60.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.971 α = 90 b = 73.971 β = 90 c = 95.07 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 100 CCD SBC-3 Si monochromator 2007-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.979508 APS 19-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.43 64.061 94.1 0.101 39.38 11.2 11200 10539 57.129
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.43 2.52 91.5 0.365 7.86 10.4 1029
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 2Q20 2.43 64.02 10622 9593 494 90.31 0.19293 0.19293 0.18927 0.1963 0.26265 0.2634 RANDOM 45.712
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] 0.51 0.26 0.51 -0.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.351 r_dihedral_angle_3_deg 19.261 r_dihedral_angle_4_deg 17.555 r_dihedral_angle_1_deg 7.739 r_scangle_it 2.77 r_scbond_it 1.876 r_angle_refined_deg 1.789 r_mcangle_it 1.169 r_angle_other_deg 0.913 r_mcbond_it 0.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.351 r_dihedral_angle_3_deg 19.261 r_dihedral_angle_4_deg 17.555 r_dihedral_angle_1_deg 7.739 r_scangle_it 2.77 r_scbond_it 1.876 r_angle_refined_deg 1.789 r_mcangle_it 1.169 r_angle_other_deg 0.913 r_mcbond_it 0.87 r_symmetry_hbond_refined 0.404 r_symmetry_vdw_other 0.207 r_nbd_other 0.197 r_nbd_refined 0.195 r_xyhbond_nbd_refined 0.189 r_nbtor_refined 0.188 r_symmetry_vdw_refined 0.16 r_mcbond_other 0.157 r_chiral_restr 0.104 r_nbtor_other 0.091 r_bond_refined_d 0.019 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1676 Nucleic Acid Atoms Solvent Atoms 88 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction SCALEPACK data scaling PHASER phasing