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Crystal Structure of the Ni-bound Human Heavy-chain variant 122H-delta C-star with meta-benzenedihyrdoxamate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5CMQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 Reservoir: 500 uL total volume: 40 mM CHES (pH 8.5), 120 mM NaCl, 0.474 mM NiCl2, 10% PEP
Sitting Drop: 7.6 uL reservoir, 2 uL of 25 uM ferritin, 2.4 uL of 5 mM
m-bdh in 50 mM CHES (pH 9.5) with 150 mM NaCl
Crystal Properties Matthews coefficient Solvent content 3.51 64.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 213.55 α = 90 b = 213.75 β = 90.048 c = 155.93 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 PIXEL DECTRIS PILATUS 6M 2016-07-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.97946 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.31 50 98.2 0.997 10.8 3.5 598668 37.69
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.31 2.37 0.503
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-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5CMQ 2.31 38.46 1.34 598248 59800 98.16 0.1929 0.187 0.1872 0.2455 0.2454 38.12
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 5.9345 f_angle_d 0.9985 f_chiral_restr 0.0484 f_bond_d 0.0089 f_plane_restr 0.0055
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 68688 Nucleic Acid Atoms Solvent Atoms 2563 Heterogen Atoms 204
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing