Experiment: 7DKP

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4KX4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.6	293.15	Protein solution: 25mg/ml in 25mM Tris pH 8.0, 150 mM NaCl, 20 mM GSH, 10 mM DHA Reservoir condition: 0.2M Ammonium acetate, 0.1M Sodium citrate tribasic dihydrate pH 5.6, 30% w/v Polyethylene glycol 4,000. Protein and reservoir mixed in 1:1, 1:2 and 2:1 ratio, set up using MRC Swissci 3 well plates with drop size of 150 nl.

Crystal Properties
Matthews coefficient	Solvent content
2.14	42.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.84	α = 90
b = 169.451	β = 93.51
c = 49.842	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 EIGER X 4M		2017-07-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-3	0.968	ESRF	MASSIF-3

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.449	42.94	94.7	0.099	0.113	0.055	0.997	8.7	4.2		137631

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.449	1.476	89.2		0.635	0.726	0.349	0.759		4.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4KX4	1.45	42.893	131485	6877	95.08	0.1394	0.1383	0.1411	0.1604	0.162	RANDOM	11.935

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]
-0.45		0.17	0.72		-0.28

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.579
r_dihedral_angle_4_deg	16.072
r_dihedral_angle_3_deg	11.312
r_dihedral_angle_1_deg	6.557
r_angle_refined_deg	1.881
r_angle_other_deg	1.687
r_chiral_restr	0.333
r_bond_refined_d	0.016
r_gen_planes_refined	0.01
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.579
r_dihedral_angle_4_deg	16.072
r_dihedral_angle_3_deg	11.312
r_dihedral_angle_1_deg	6.557
r_angle_refined_deg	1.881
r_angle_other_deg	1.687
r_chiral_restr	0.333
r_bond_refined_d	0.016
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6813
Nucleic Acid Atoms
Solvent Atoms	1314
Heterogen Atoms	119

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	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.