☰ Navigation Tabs
Crystal Structure of the Zn-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: 25 mM CHES (pH 8.5), 75 mM NaCl,
0.474 mM ZnCl2, 10% PEP
Sitting Drop: 7.6 uL reservoir, 2 uL of 25 uM ferritin, 2.4 uL of 5 mM
H2fdh in 50 mM CHES (pH 9.5) with 150 mM NaCl
Crystal Properties Matthews coefficient Solvent content 3.53 65.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 213.99 α = 90 b = 213.9 β = 90.136 c = 156.33 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 2016-01-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.9795 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 2.34 50 94.7 0.997 13.24 3.4 558216 35.02
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 2.34 2.4 0.761
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 2.34 38.49 1.42 558006 55666 94.66 0.2142 0.2071 0.2075 0.2778 0.2775 35.25
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 20.4317 f_angle_d 1.0632 f_chiral_restr 0.0496 f_bond_d 0.0095 f_plane_restr 0.0057
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 68688 Nucleic Acid Atoms Solvent Atoms 1764 Heterogen Atoms 244
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing