Experiment: 3NK5

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	298	25-30% PEG2000,100mM sodium cacodylate, 50-100mM MgCl2, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.51	64.93

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 92.424	α = 90
b = 92.424	β = 90
c = 78.819	γ = 90

Symmetry
Space Group	P 4

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	103	CCD	ADSC QUANTUM 210	monochrometer	2006-10-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1	0.97949	ALS	8.3.1

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	2.4	92.45	95.4	0.074	0.074	15.4	3.2	24848	24848		3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.4	2.53	86.6		0.699	0.699	1.1	2.9	3281

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	PDB entry 209F	2.4	19.99	24847	1264	95.27	0.1831	0.1812	0.2203	RANDOM	49.589

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]
0.03			0.03		-0.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.054
r_dihedral_angle_4_deg	21.568
r_dihedral_angle_3_deg	15.739
r_dihedral_angle_1_deg	6.161
r_scangle_it	2.91
r_scbond_it	1.985
r_angle_refined_deg	1.712
r_angle_other_deg	1.161
r_mcangle_it	1.135
r_mcbond_it	0.646

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.054
r_dihedral_angle_4_deg	21.568
r_dihedral_angle_3_deg	15.739
r_dihedral_angle_1_deg	6.161
r_scangle_it	2.91
r_scbond_it	1.985
r_angle_refined_deg	1.712
r_angle_other_deg	1.161
r_mcangle_it	1.135
r_mcbond_it	0.646
r_mcbond_other	0.192
r_chiral_restr	0.099
r_bond_refined_d	0.02
r_gen_planes_refined	0.01
r_gen_planes_other	0.003
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3356
Nucleic Acid Atoms
Solvent Atoms	136
Heterogen Atoms	80

Software

Software
Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ELVES	refinement
ELVES	data reduction

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.