Experiment: 4JDS

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1O9S

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	291	25% PEG 3350, 0.1 M Ammonium Sulfate, 0.1 M BisTris pH6.5, vapor diffusion hanging drop, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.29	46.38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 118.048	α = 90
b = 134.482	β = 90
c = 137.255	γ = 90

Symmetry
Space Group	C 2 2 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 CCD300		2012-01-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	0.97949	CLSI	08ID-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.7	50	99.7	0.089	0.089	26.3	7.4		119046			21.8

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	1.7	1.73	99.4		0.635		7	5879

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	1O9S	1.7	50	118841	1202	99.45	0.1988	0.1986	0.2226	RANDOM	24.8969

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]
-0.11			0.64		-0.53

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.422
r_dihedral_angle_3_deg	11.947
r_dihedral_angle_4_deg	9.708
r_dihedral_angle_1_deg	5.551
r_scangle_it	2.657
r_scbond_it	1.598
r_mcangle_it	1.128
r_angle_refined_deg	1.108
r_mcbond_it	0.591
r_chiral_restr	0.072

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.422
r_dihedral_angle_3_deg	11.947
r_dihedral_angle_4_deg	9.708
r_dihedral_angle_1_deg	5.551
r_scangle_it	2.657
r_scbond_it	1.598
r_mcangle_it	1.128
r_angle_refined_deg	1.108
r_mcbond_it	0.591
r_chiral_restr	0.072
r_bond_refined_d	0.008
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7552
Nucleic Acid Atoms
Solvent Atoms	953
Heterogen Atoms	273

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
MOLREP	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.