Experiment: 5NCH

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3EMR	Ensembled model from: 3EMR, 2A1X, 2FCT, 3GJB, 2OPW
experimental model	PDB	2A1X	Ensembled model from: 3EMR, 2A1X, 2FCT, 3GJB, 2OPW
experimental model	PDB	2FCT	Ensembled model from: 3EMR, 2A1X, 2FCT, 3GJB, 2OPW
experimental model	PDB	3GJB	Ensembled model from: 3EMR, 2A1X, 2FCT, 3GJB, 2OPW
experimental model	PDB	2OPW	Ensembled model from: 3EMR, 2A1X, 2FCT, 3GJB, 2OPW

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	285	20.8 % (w/v) PEG 4000, 0.233 M LiSO4, 0.1 M HEPES/NaOH pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
2.55	51.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.365	α = 90
b = 69.837	β = 90.18
c = 98.378	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	CCD	RIGAKU SATURN 944+	VariMax HF	2013-02-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.54183

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	1.819	98.378	86.3	0.081	0.05	0.997	11.4	3.5		46652

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	1.819	1.85	84		0.711	0.459	0.786	2.2	3.4

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	Ensembled model from: 3EMR, 2A1X, 2FCT, 3GJB, 2OPW	1.819	40.49	1.34	46611	2301	86.2	0.1743	0.1722	0.2128	Random selection

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	15.014
f_angle_d	0.81
f_chiral_restr	0.052
f_bond_d	0.007
f_plane_restr	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3893
Nucleic Acid Atoms
Solvent Atoms	518
Heterogen Atoms

Software

Software
Software Name	Purpose
PHENIX	refinement
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.