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Crystal structure of cardiotoxic Bence-Jones light chain dimer H9
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JVK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 293 0.1 M Sodium citrate, 16 % w/v PEG 4000, 10 % v/v 2-Propanol
Crystal Properties Matthews coefficient Solvent content 2.85 56.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.492 α = 95.32 b = 63.429 β = 85.84 c = 86.637 γ = 99.58
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 PIXEL DECTRIS PILATUS 6M 2015-11-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.979 ESRF ID29
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 1.64 45.77 95.7 0.087 7.3 3.6 113757 22.59
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 1.64 1.7 94.2 0.54 1.6 3.7
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 1JVK 1.64 45.77 113747 5715 95.7 0.184 0.183 0.1877 0.203 0.208 RANDOM 25.75
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] 0.1756 -0.1579 0.4902 0.0102 -0.2228 -0.1858
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 15.06 t_omega_torsion 4.04 t_angle_deg 1.14 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 15.06 t_omega_torsion 4.04 t_angle_deg 1.14 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6235 Nucleic Acid Atoms Solvent Atoms 882 Heterogen Atoms 39
Software Software Software Name Purpose BUSTER refinement XDS data reduction SCALA data scaling PHASER phasing