Experiment: 5J62

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	295	0.1 M sodium citrate, pH 5.6 10% PEG 1500

Crystal Properties
Matthews coefficient	Solvent content
2.41	48.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.323	α = 90
b = 100.323	β = 90
c = 99.921	γ = 90

Symmetry
Space Group	P 41 21 2

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		2015-05-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL12-2	0.98	SSRL	BL12-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.15	50	100	0.076	0.078	0.016	6.6	23.9		28386

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.15	2.19	99.9		0.742	0.775	0.218	0.816		11.9	1388

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	ensemble model of 3PXV and 3EK3	2.15	35.47	26891	1415	99.81	0.1698	0.1673	0.2175	RANDOM	45.286

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]
0.23			0.23		-0.45

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.896
r_dihedral_angle_3_deg	15.609
r_dihedral_angle_4_deg	8.659
r_dihedral_angle_1_deg	5.865
r_mcangle_it	5.489
r_mcbond_it	3.998
r_mcbond_other	3.975
r_angle_refined_deg	1.766
r_angle_other_deg	1.041
r_chiral_restr	0.117

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.896
r_dihedral_angle_3_deg	15.609
r_dihedral_angle_4_deg	8.659
r_dihedral_angle_1_deg	5.865
r_mcangle_it	5.489
r_mcbond_it	3.998
r_mcbond_other	3.975
r_angle_refined_deg	1.766
r_angle_other_deg	1.041
r_chiral_restr	0.117
r_bond_refined_d	0.017
r_gen_planes_refined	0.01
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3259
Nucleic Acid Atoms
Solvent Atoms	138
Heterogen Atoms	73

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	phasing
PHASER	phasing
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	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 R01GM133198.