Experiment: 4DJH

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3ODU	poly Ala model of PDB entry 3ODU. ensemble of T4L models from PDB entries 2RH1, 3EML,3ODU, 3PBL, and 3RZE.
experimental model	PDB	2RH1	poly Ala model of PDB entry 3ODU. ensemble of T4L models from PDB entries 2RH1, 3EML,3ODU, 3PBL, and 3RZE.
experimental model	PDB	3EML	poly Ala model of PDB entry 3ODU. ensemble of T4L models from PDB entries 2RH1, 3EML,3ODU, 3PBL, and 3RZE.
experimental model	PDB	3PBL	poly Ala model of PDB entry 3ODU. ensemble of T4L models from PDB entries 2RH1, 3EML,3ODU, 3PBL, and 3RZE.
experimental model	PDB	3RZE	poly Ala model of PDB entry 3ODU. ensemble of T4L models from PDB entries 2RH1, 3EML,3ODU, 3PBL, and 3RZE.

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	LIPIDIC CUBIC PHASE	6	293	100 mM sodium citrate pH 6.0, 30% (v/v) PEG400, 400 mM potassium nitrate, lipidic cubic phase, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.82	67.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.896	α = 90
b = 147.297	β = 90
c = 205.288	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 300 mm CCD	double crystal monochromator and K-B pair of biomorph mirrors for vertical and horizontal focusing	2011-12-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	1.0330	APS	23-ID-D

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	2.9	50	97.1	0.18	12.6	5.6		38323

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	2.9	3	87.5		0.95	1.3	3.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	poly Ala model of PDB entry 3ODU. ensemble of T4L models from PDB entries 2RH1, 3EML,3ODU, 3PBL, and 3RZE.	2.9	35.861	1.33	37023	1851	97.8	0.2285	0.2266	0.2646

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]
6.5962			-2.379		-4.2172

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	13.168
f_angle_d	0.767
f_chiral_restr	0.039
f_bond_d	0.005
f_plane_restr	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6932
Nucleic Acid Atoms
Solvent Atoms	25
Heterogen Atoms	132

Software

Software
Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
PHENIX	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.