Experiment: 5NNX

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4Z8E

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.24	298	Ammonium Sulphate, MOPS, PEG (6000), PME(550)

Crystal Properties
Matthews coefficient	Solvent content
4.87	74.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 112.3	α = 90
b = 112.3	β = 90
c = 157.562	γ = 120

Symmetry
Space Group	H 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	100	CCD	ADSC QUANTUM 315		2016-04-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.97242	ESRF	ID23-1

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	3.29	46.46	97.4	0.079	0.087	0.035	1	9.8	5.9		5806

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	3.29	3.55	93.6		2.218	2.442	0.992	0.503		5.7

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4Z8E	3.29	46	5205	601	96.51	0.2032	0.1955	0.2777	RANDOM	167.303

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]
1.02	0.51		1.02		-3.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.137
r_dihedral_angle_3_deg	24.422
r_dihedral_angle_1_deg	22.746
r_dihedral_angle_4_deg	18.329
r_angle_refined_deg	1.65
r_angle_other_deg	1.499
r_chiral_restr	0.249
r_bond_refined_d	0.032
r_gen_planes_refined	0.012
r_bond_other_d	0.003

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.137
r_dihedral_angle_3_deg	24.422
r_dihedral_angle_1_deg	22.746
r_dihedral_angle_4_deg	18.329
r_angle_refined_deg	1.65
r_angle_other_deg	1.499
r_chiral_restr	0.249
r_bond_refined_d	0.032
r_gen_planes_refined	0.012
r_bond_other_d	0.003
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	602
Nucleic Acid Atoms	738
Solvent Atoms	56
Heterogen Atoms

Software

Software
Software Name	Purpose
Aimless	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
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 R01GM133198.