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kI O18/O8 Y87H 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 8.1 295 1.2 M sodium citrate in 0.1 M Tris buffer, pH 8.1, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 3.18 61.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.959 α = 90 b = 98.043 β = 119.6 c = 73.074 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 IMAGE PLATE RIGAKU RAXIS IV++ Osmic Varimax 2007-12-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.5241
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 1.39 34.52 73.7 0.043 14.5 3.31 177610 130900
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) 1.39 1.44 13.9 0.325 1.9 1.82
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 (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 1.53 17.56 177610 43135 2279 99.93 0.19118 0.18904 0.1714 0.23147 0.2159 RANDOM 24.79
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] 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.943 r_dihedral_angle_1_deg 14.494 r_dihedral_angle_4_deg 14.25 r_dihedral_angle_3_deg 12.578 r_sphericity_free 7.39 r_scangle_it 4.988 r_sphericity_bonded 4.824 r_scbond_it 3.552 r_mcangle_it 2.678 r_angle_refined_deg 1.858
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.943 r_dihedral_angle_1_deg 14.494 r_dihedral_angle_4_deg 14.25 r_dihedral_angle_3_deg 12.578 r_sphericity_free 7.39 r_scangle_it 4.988 r_sphericity_bonded 4.824 r_scbond_it 3.552 r_mcangle_it 2.678 r_angle_refined_deg 1.858 r_mcbond_it 1.806 r_rigid_bond_restr 1.652 r_nbtor_refined 0.31 r_nbd_refined 0.216 r_symmetry_vdw_refined 0.208 r_xyhbond_nbd_refined 0.167 r_symmetry_hbond_refined 0.158 r_chiral_restr 0.155 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5536 Nucleic Acid Atoms Solvent Atoms 1056 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection CrystalClear data reduction CrystalClear data scaling PHASER phasing