Experiment: 3NKA

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	298	25-30% PEG 2000 100 mM sodium cacodylate 50-100 mM MgCl2, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.54	65.27

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 92.784	α = 90
b = 92.784	β = 90
c = 78.919	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	2.5	92.848	93.8	0.063	0.063	17.4	3.4	21743	21743		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)
1	2.5	2.64	82.4		0.645	0.645	1.2	3.5	2743

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 2O9F	2.5	20	21742	1120	93.41	0.188	0.1862	0.2206	RANDOM	55.675

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
r_dihedral_angle_2_deg	34.021
r_dihedral_angle_4_deg	27.803
r_dihedral_angle_3_deg	15.173
r_dihedral_angle_1_deg	6.259
r_scangle_it	2.858
r_scbond_it	1.923
r_angle_refined_deg	1.729
r_angle_other_deg	1.42
r_mcangle_it	1.121
r_mcbond_it	0.617

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.021
r_dihedral_angle_4_deg	27.803
r_dihedral_angle_3_deg	15.173
r_dihedral_angle_1_deg	6.259
r_scangle_it	2.858
r_scbond_it	1.923
r_angle_refined_deg	1.729
r_angle_other_deg	1.42
r_mcangle_it	1.121
r_mcbond_it	0.617
r_mcbond_other	0.166
r_chiral_restr	0.095
r_bond_refined_d	0.021
r_gen_planes_refined	0.01
r_bond_other_d	0.005
r_gen_planes_other	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3357
Nucleic Acid Atoms
Solvent Atoms	75
Heterogen Atoms	98

Software

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