Experiment: 2PNJ

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH	6.5	291	MICROBATCH UNDER OIL (70:30 PARAFFIN/SILICONE OIL MIXTURE) METHO USING 2 microliter DROPS CONTAINING EQUAL VOLUMES OF PROTEIN SOLUTION (64 MG/ML IN 50 MM TRIS MOPS, 0.1M KCL, 1% NA-CHOLATE, 250 MM IMIDAZOLE, PH 8.1) AND PRECIPITANT SOLUTION (0.2 M SODIUM ACETAT TRI HYDRATE, 0.1 M SODIUM CACODYLATE, PH 6.5 IN 30%W/V POLYETHYL GLYCOL 8000 (HAMPTON CRYSTAL SCREEN I-28, HAMPTON RESEARCH), pH 6.50, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.81	56.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.686	α = 90
b = 94.052	β = 90
c = 113.276	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 225 mm CCD	ROSENBAUM	2005-11-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-BM	1.00	APS	22-BM

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	50	90.1	0.057	25.23	17.5		58933

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	2.07	98.2		0.242	3.39	10

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 Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	DIFFERENCE FOURIER	THROUGHOUT	1HRK	2.35	43.44	36722	36722	1944	96.36	0.19473	0.19473	0.19168	0.4	0.25332	RANDOM	25.034

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]
			-0.02		0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.657
r_dihedral_angle_4_deg	18.854
r_dihedral_angle_3_deg	16.35
r_dihedral_angle_1_deg	11.82
r_scangle_it	3.383
r_scbond_it	2.26
r_angle_refined_deg	1.82
r_mcangle_it	1.392
r_mcbond_it	0.865
r_nbtor_refined	0.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.657
r_dihedral_angle_4_deg	18.854
r_dihedral_angle_3_deg	16.35
r_dihedral_angle_1_deg	11.82
r_scangle_it	3.383
r_scbond_it	2.26
r_angle_refined_deg	1.82
r_mcangle_it	1.392
r_mcbond_it	0.865
r_nbtor_refined	0.31
r_nbd_refined	0.223
r_xyhbond_nbd_refined	0.194
r_symmetry_vdw_refined	0.19
r_chiral_restr	0.108
r_symmetry_hbond_refined	0.093
r_bond_refined_d	0.016
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5642
Nucleic Acid Atoms
Solvent Atoms	342
Heterogen Atoms	182

Software

Software
Software Name	Purpose
SERGUI	data collection
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	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.