Experiment: 4PNG

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	298	0.1 M Tris HCl pH 7.5, 25% w/v PEG4000, 2 mM GSH, 10 mM DTT

Crystal Properties
Matthews coefficient	Solvent content
2.04	39.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.731	α = 90
b = 87.09	β = 90
c = 87.226	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	PIXEL	PSI PILATUS 6M		2013-12-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.987	SSRL	BL11-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	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	1.53	34.58	96.5	0.046	0.024	0.999	21.1	4.5		63530

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.53	1.56	55.8		0.372	0.238	0.828	2.9	2.9	1779

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	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		THROUGHOUT	1.53	34.58	63467	3223	96.17	0.16	0.1584	0.17	0.1907	0.2	RANDOM	15.377

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]
0.22			-0.38		0.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.067
r_dihedral_angle_4_deg	22.35
r_dihedral_angle_3_deg	14.07
r_dihedral_angle_1_deg	5.483
r_angle_other_deg	1.897
r_mcangle_it	1.772
r_angle_refined_deg	1.433
r_mcbond_it	1.058
r_mcbond_other	1.057
r_chiral_restr	0.123

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.067
r_dihedral_angle_4_deg	22.35
r_dihedral_angle_3_deg	14.07
r_dihedral_angle_1_deg	5.483
r_angle_other_deg	1.897
r_mcangle_it	1.772
r_angle_refined_deg	1.433
r_mcbond_it	1.058
r_mcbond_other	1.057
r_chiral_restr	0.123
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3577
Nucleic Acid Atoms
Solvent Atoms	403
Heterogen Atoms	42

Software

Software
Software Name	Purpose
XDS	data reduction
REFMAC	refinement
PDB_EXTRACT	data extraction
XSCALE	data scaling
Aimless	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.