Experiment: 2PN4

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2PN3	PDB ENTRY 2PN3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	EVAPORATION	6.2	290	30% MPD, 80mM SrCl2, 25mM NaCl, 50mM Cacodylate equilibrated with 60%MPD, pH 6.2, EVAPORATION, temperature 290.0K

Crystal Properties
Matthews coefficient	Solvent content
2.48	50.48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.286	α = 90
b = 48.73	β = 90
c = 119.999	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	77	CCD	ADSC QUANTUM 315	mirrors	2006-03-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 8-BM	0.97949	APS	8-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	2.32	59.98	95.9	0.108	17.5	5.5	12751	12228			59.9

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	2.32	2.43	100		0.714	2.4	6.9	1247

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 (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2PN3	2.32	59.98	12210	11590	598	94.92	0.26515	0.26405	0.26141	0.26	0.32037	0.32	RANDOM	51.272

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]
-2.24			-0.38		2.62

RMS Deviations
Key	Refinement Restraint Deviation
r_scangle_it	1.94
r_angle_refined_deg	1.835
r_scbond_it	1.409
r_symmetry_hbond_refined	0.317
r_nbtor_refined	0.279
r_metal_ion_refined	0.222
r_nbd_refined	0.165
r_symmetry_vdw_refined	0.164
r_xyhbond_nbd_refined	0.162
r_chiral_restr	0.078

RMS Deviations
Key	Refinement Restraint Deviation
r_scangle_it	1.94
r_angle_refined_deg	1.835
r_scbond_it	1.409
r_symmetry_hbond_refined	0.317
r_nbtor_refined	0.279
r_metal_ion_refined	0.222
r_nbd_refined	0.165
r_symmetry_vdw_refined	0.164
r_xyhbond_nbd_refined	0.162
r_chiral_restr	0.078
r_bond_refined_d	0.01
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	1860
Solvent Atoms	67
Heterogen Atoms	10

Software

Software
Software Name	Purpose
REFMAC	refinement
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

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.