Experiment: 6CDD

Npl4 zinc finger and MPN domains (Chaetomium thermophilum)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		cryo-EM density

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	277	0.2 M Na/K phosphate pH 7, 9.2% wt/vol poly-gamma-glutamic acid, 0.2 M potassium thiocyanate, 5% propylene glycol

Crystal Properties
Matthews coefficient	Solvent content
3.81	67.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.858	α = 90
b = 72.221	β = 96.714
c = 193.543	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-F		2017-08-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-C	1.283	APS	24-ID-C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.582	96.11	95.15	0.06434	0.04406	0.998	9.82	2.9		96089			81.4323024304

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.582	2.675	77.79		2.031	1.443	0.322		2.7

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	cryo-EM density	2.58233712092	96.107851877	1.33489028264	94503	4617	95.1528942678	0.193296283219	0.19152216146	0.2028	0.228609406897	0.2364	105.883376985

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	16.932750883
f_angle_d	0.529373849969
f_chiral_restr	0.0418141893585
f_plane_restr	0.00262453528802
f_bond_d	0.00229496813905

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7283
Nucleic Acid Atoms
Solvent Atoms	228
Heterogen Atoms	4

Software

Software
Software Name	Purpose
XDS	data scaling
PHENIX	refinement
PHENIX	phasing
Coot	model building