Experiment: 5DLT

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2XR9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	293	PEG 3350, 0.1M ammonium iodide 0.3M sodium thiocyanate, 23.5mg/ml heparin sulfate

Crystal Properties
Matthews coefficient	Solvent content
2.35	47.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.671	α = 98.72
b = 63.482	β = 105.8
c = 70.715	γ = 99.97

Symmetry
Space Group	P 1

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	DECTRIS PILATUS 6M-F		2011-08-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.97935	ESRF	ID29

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	1.6	44.02	92.1	0.065	0.061	0.997	6.7	2		105202			29.61

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	1.6	1.63	88.9		0.868	0.815	0.437	0.8	1.9	5091

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2xr9	1.6	44.02	99938	5262	92.11	0.1725	0.1713	0.18	0.1964	0.21	RANDOM	28.789

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	-0.02	0.33	0.21	0.1	-0.56

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.694
r_dihedral_angle_4_deg	16.806
r_dihedral_angle_3_deg	12.18
r_sphericity_bonded	11.517
r_dihedral_angle_1_deg	6.214
r_mcangle_it	2.295
r_mcbond_it	1.491
r_mcbond_other	1.467
r_angle_refined_deg	1.45
r_angle_other_deg	0.955

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.694
r_dihedral_angle_4_deg	16.806
r_dihedral_angle_3_deg	12.18
r_sphericity_bonded	11.517
r_dihedral_angle_1_deg	6.214
r_mcangle_it	2.295
r_mcbond_it	1.491
r_mcbond_other	1.467
r_angle_refined_deg	1.45
r_angle_other_deg	0.955
r_chiral_restr	0.085
r_bond_refined_d	0.012
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6431
Nucleic Acid Atoms
Solvent Atoms	528
Heterogen Atoms	158

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
Aimless	data scaling
XDS	data reduction
PHASER	phasing
Coot	model building

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.