Experiment: 2R9S

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH	5.5	298	25-32% PEG 3350, 100mM NaCl, 1mM AMP-PCP, 2mM MgCl2, 0.4mM Zwittergent 314, 10%(v/v) ethylene glycol, pH 5.5, microbatch, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.08	40.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.318	α = 90
b = 81.344	β = 90
c = 123.76	γ = 90

Symmetry
Space Group	P 21 21 21

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	MARMOSAIC 325 mm CCD		2007-04-10		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.997	SSRL	BL11-1

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	2.27	50	99.2	0.056	15.6	6.9		32372			41.67

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	2.27	2.35	93.9		0.507		4.7	3005

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		THROUGHOUT	PDB Entry 1JNK	2.4	38.63	27603	1390	99.84	0.209	0.205	0.29	RANDOM	45.866

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]
0.33			-0.26		-0.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.241
r_dihedral_angle_4_deg	19.606
r_dihedral_angle_3_deg	18.469
r_dihedral_angle_1_deg	7.83
r_scangle_it	3.715
r_scbond_it	2.519
r_angle_refined_deg	1.944
r_mcangle_it	1.62
r_mcbond_it	1.048
r_symmetry_hbond_refined	0.377

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.241
r_dihedral_angle_4_deg	19.606
r_dihedral_angle_3_deg	18.469
r_dihedral_angle_1_deg	7.83
r_scangle_it	3.715
r_scbond_it	2.519
r_angle_refined_deg	1.944
r_mcangle_it	1.62
r_mcbond_it	1.048
r_symmetry_hbond_refined	0.377
r_nbtor_refined	0.312
r_symmetry_vdw_refined	0.237
r_nbd_refined	0.235
r_xyhbond_nbd_refined	0.186
r_chiral_restr	0.139
r_bond_refined_d	0.025
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5362
Nucleic Acid Atoms
Solvent Atoms	182
Heterogen Atoms	125

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
PHASER	phasing

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.