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STRUCTURE OF THE VARIABLE DOMAIN OF HUMAN IMMUNOGLOBULIN K-4 LIGHT CHAIN LEN
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LVE 1LVE WITH GLN89 CHANGED TO ALA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 2.0 M AMMONIUM SULFATE, 0.1M HEPES PH 7.5, 1MM ZINC ACETATE
Crystal Properties Matthews coefficient Solvent content 3 59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.3 α = 90 b = 106.3 β = 90 c = 45.1 γ = 120
Symmetry Space Group P 62 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 IMAGE PLATE RIGAKU MIRRORS 1998-06-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200
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 30 97 0.074 25 10 7471 6.6
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) 1 2 2.07 88.3 0.242 6.8 15.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1LVE WITH GLN89 CHANGED TO ALA 2 8 3 9087 949 87.5 0.186 0.2045 0.218 RANDOM 18.6
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] -1.32 -3.57 -1.32 2.63
RMS Deviations Key Refinement Restraint Deviation x_dihedral_angle_d 26.1 x_scangle_it 1.81 x_angle_deg 1.4 x_mcangle_it 1.2 x_scbond_it 1.18 x_improper_angle_d 0.77 x_mcbond_it 0.72 x_bond_d 0.005 x_bond_d_na x_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation x_dihedral_angle_d 26.1 x_scangle_it 1.81 x_angle_deg 1.4 x_mcangle_it 1.2 x_scbond_it 1.18 x_improper_angle_d 0.77 x_mcbond_it 0.72 x_bond_d 0.005 x_bond_d_na x_bond_d_prot x_angle_d x_angle_d_na x_angle_d_prot x_angle_deg_na x_angle_deg_prot x_dihedral_angle_d_na x_dihedral_angle_d_prot x_improper_angle_d_na x_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 883 Nucleic Acid Atoms Solvent Atoms 156 Heterogen Atoms 1
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling AMoRE phasing CNS refinement