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Wild type immunoglobulin light chain (WT-1)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4NKI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 0.1M HEPES, 0.2 M CaCl2, 28% PEG 400
Crystal Properties Matthews coefficient Solvent content 3.77 67.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.5 α = 90 b = 104.5 β = 90 c = 55.22 γ = 120
Symmetry Space Group P 63 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 6M 2016-10-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.97625 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 1.55 50 99.7 0.046 0.999 20.9 6.2 26220
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.55 1.65 99.8 0.587 0.868 3.2
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 4NKI 1.55 15 24867 1309 99.57 0.143 0.1418 0.155 0.1649 0.1787 RANDOM 25.416
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] 0.28 0.14 0.28 -0.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.923 r_sphericity_free 21.632 r_dihedral_angle_4_deg 21.621 r_dihedral_angle_3_deg 11.125 r_sphericity_bonded 6.944 r_dihedral_angle_1_deg 6.325 r_angle_refined_deg 1.315 r_rigid_bond_restr 1.131 r_angle_other_deg 0.875 r_chiral_restr 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.923 r_sphericity_free 21.632 r_dihedral_angle_4_deg 21.621 r_dihedral_angle_3_deg 11.125 r_sphericity_bonded 6.944 r_dihedral_angle_1_deg 6.325 r_angle_refined_deg 1.315 r_rigid_bond_restr 1.131 r_angle_other_deg 0.875 r_chiral_restr 0.08 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 811 Nucleic Acid Atoms Solvent Atoms 173 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling PHASER phasing