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Crystal Structure of the Ni-bound Human Heavy-chain variant 122H-delta C-star with 2,5-furandihyrdoxamate 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: 31 mM CHES (pH 10), 93 mM NaCl,
0.474 mM NiCl2, 12% PEP
Sitting Drop: 7.6 uL reservoir, 2 uL of 25 uM ferritin, 2.4 uL of 10 mM
H2fdh in 50 mM CHES (pH 9.5) with 150 mM NaCl
Crystal Properties Matthews coefficient Solvent content 3.74 67.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 155.99 α = 90 b = 155.99 β = 90 c = 155.99 γ = 90
Symmetry Space Group I 4 3 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 PILATUS 6M 2016-11-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.97946 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 2.68 36.77 99.2 0.994 7.1 4.9 9313 58.17
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 2.68 2.81 0.87
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 2.68 36.77 1.34 9262 458 98.19 0.1993 0.197 0.1975 0.2444 0.2405 65.63
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 7.1328 f_angle_d 1.2082 f_chiral_restr 0.0557 f_bond_d 0.0124 f_plane_restr 0.0066
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1429 Nucleic Acid Atoms Solvent Atoms 26 Heterogen Atoms 17
Software Software Software Name Purpose PHENIX refinement iMOSFLM data reduction Aimless data scaling PHASER phasing