7JGO | pdb_00007jgo

Crystal Structure of the Ni-bound Human Heavy-chain variant 122H-delta C-star with 2,5-furandihyrdoxamate collected at 278K

X-RAY DIFFRACTION

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	9.5	298	Reservoir: 500 uL total volume: 50 mM CHES (pH 9.5), 150 mM NaCl, 0.474 mM NiCl2, 12.6% PEP Sitting Drop: 12.7 uL reservoir, 3.3 uL of 25 uM ferritin, 4 uL of 10 mM fdh in 50 mM CHES (pH 9.5) with 150 mM NaCl

Crystal Properties
Matthews coefficient	Solvent content
3.75	67.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 156.082	α = 90
b = 156.082	β = 90
c = 156.082	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	278	CCD	APEX II CCD		2019-09-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER AXS MICROSTAR	1.54178

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	3.08	49.36	100	0.996	9.8	18.4		11398			48.66

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	3.08	3.19			0.899

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	3.08	49.36	1.33	10860	1104	95.31	0.2127	0.2086	0.21	0.2482	0.25	39.25

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	7.0615
f_angle_d	0.7588
f_chiral_restr	0.0438
f_bond_d	0.0053
f_plane_restr	0.0036

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1425
Nucleic Acid Atoms
Solvent Atoms	25
Heterogen Atoms	17

Software

Software
Software Name	Purpose
PHENIX	refinement
SAINT	data reduction
SADABS	data scaling
PHASER	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.