Experiment: 3NDF

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1EZX	PDB ENTRY 1EZX

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6.5	295	0.12M Alcohols (Morpheus), 0.1M Buffer 1, 13.3% PEG 550MME, 6.6% PEG 20000, 20% glycerol, pH 6.5, VAPOR DIFFUSION, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.09

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 37.45	α = 90
b = 83.27	β = 99.66
c = 61.09	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	IMAGE PLATE	MAR scanner 345 mm plate		2009-02-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	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	2.7	48.8	96.6	0.042	0.042			9871	9871

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.7	2.85	99.4		0.129	6.1	1.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	PDB ENTRY 1EZX	2.7	48.8	9871	8867	989	96.25	0.21662	0.21662	0.21085	0.21	0.26787	0.26	RANDOM	20.298

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]
-1.07		0.34	0.36		0.82

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.578
r_dihedral_angle_3_deg	12.086
r_dihedral_angle_4_deg	10.159
r_dihedral_angle_1_deg	4.042
r_scangle_it	0.674
r_angle_refined_deg	0.617
r_mcangle_it	0.379
r_scbond_it	0.372
r_mcbond_it	0.203
r_chiral_restr	0.045

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.578
r_dihedral_angle_3_deg	12.086
r_dihedral_angle_4_deg	10.159
r_dihedral_angle_1_deg	4.042
r_scangle_it	0.674
r_angle_refined_deg	0.617
r_mcangle_it	0.379
r_scbond_it	0.372
r_mcbond_it	0.203
r_chiral_restr	0.045
r_bond_refined_d	0.003
r_gen_planes_refined	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2828
Nucleic Acid Atoms
Solvent Atoms	22
Heterogen Atoms

Software

Software
Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

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.