Experiment: 4NEK

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	PEG550 30%, 0.05 M Magnesium chloride hexahydrate, HEPES 0.1M pH 7.5, 1.5 M NaCl, vapor diffusion, sitting drop, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.66	53.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.285	α = 90
b = 156.683	β = 113.81
c = 79.297	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	ADSC QUANTUM 315r	mirrors	2013-06-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97912	APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.3	40	99.3	0.147	7	5.1		74539

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)
1	2.3	2.34	93.1		0.868		3.4	3478

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	SAD	THROUGHOUT	2.3	40	64853	3263	86.31	0.178	0.1764	0.2073	RANDOM	35.8687

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]
-0.69		-0.64	0.87		0.27

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.517
r_dihedral_angle_4_deg	16.881
r_dihedral_angle_3_deg	13.401
r_dihedral_angle_1_deg	5.656
r_mcangle_it	3.803
r_mcbond_it	2.52
r_mcbond_other	2.519
r_angle_refined_deg	1.581
r_angle_other_deg	1.22
r_chiral_restr	0.082

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.517
r_dihedral_angle_4_deg	16.881
r_dihedral_angle_3_deg	13.401
r_dihedral_angle_1_deg	5.656
r_mcangle_it	3.803
r_mcbond_it	2.52
r_mcbond_other	2.519
r_angle_refined_deg	1.581
r_angle_other_deg	1.22
r_chiral_restr	0.082
r_bond_refined_d	0.014
r_gen_planes_refined	0.009
r_bond_other_d	0.007
r_gen_planes_other	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11169
Nucleic Acid Atoms
Solvent Atoms	386
Heterogen Atoms	35

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data collection

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.