Experiment: 5TR4

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3CMM

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	298	70 mM Na malonate pH 6.0, 70 mM malic acid, 70 mM Na citrate, 10-15% peg-3350

Crystal Properties
Matthews coefficient	Solvent content
2.97	58.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 212.485	α = 90
b = 172.148	β = 90
c = 79.424	γ = 90

Symmetry
Space Group	P 21 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 225 mm CCD		2010-08-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.97929	APS	31-ID

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	2.2	50	98.8	0.14	0.151	0.056	6	6.9		146857

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.28	97		1.164	0.616		6.7

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	3CMM	2.2	50	139402	2842	95.65	0.2171	0.2163	0.2559	RANDOM	34.902

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]
-0.34			0.01		0.33

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.386
r_dihedral_angle_4_deg	17.56
r_dihedral_angle_3_deg	13.745
r_dihedral_angle_1_deg	5.735
r_mcangle_it	4.769
r_scbond_it	4.254
r_mcbond_it	3.412
r_angle_refined_deg	1.303
r_chiral_restr	0.084
r_bond_refined_d	0.009

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.386
r_dihedral_angle_4_deg	17.56
r_dihedral_angle_3_deg	13.745
r_dihedral_angle_1_deg	5.735
r_mcangle_it	4.769
r_scbond_it	4.254
r_mcbond_it	3.412
r_angle_refined_deg	1.303
r_chiral_restr	0.084
r_bond_refined_d	0.009
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	15867
Nucleic Acid Atoms
Solvent Atoms	404
Heterogen Atoms	68

Software

Software
Software Name	Purpose
HKL-2000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
MOLREP	phasing
HKL	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.