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Crystal Structure of the Zn-bound Human Heavy-chain variant 122H-delta C-star with meta-benzenedihyrdoxamate collected at 100K
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: 50 mM CHES (pH 9.5), 150 mM NaCl, 0.474 mM ZnCl2, 12.6% PEP
Sitting Drop: 7.6 uL reservoir, 2 uL of 25 uM ferritin, 2.4 uL of 10 mM
m-bdh in 50 mM CHES (pH 9.5) with 150 mM NaCl
Crystal Properties Matthews coefficient Solvent content 3.59 65.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 215.75 α = 90 b = 215.46 β = 89.952 c = 156.46 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 2018-06-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.9795 SSRL BL9-2
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 2.07 50 97.6 0.997 9.95 3.5 843866 29.68
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 2.07 2.12 0.541
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 2.07 37.8 1.34 843340 84342 97.52 0.1889 0.1843 0.1842 0.2292 0.2288 29.8
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 5.5464 f_angle_d 0.8978 f_chiral_restr 0.046 f_bond_d 0.0083 f_plane_restr 0.0052
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 68688 Nucleic Acid Atoms Solvent Atoms 4842 Heterogen Atoms 252
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing