Experiment: 5DQ9

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4ODS

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4	289	1M LiCl, 0.1M citric acid, and 20% (w/v) PEG 6000

Crystal Properties
Matthews coefficient	Solvent content
2.32	47.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 338.121	α = 90
b = 52.865	β = 100.95
c = 75.391	γ = 90

Symmetry
Space Group	C 1 2 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	IMAGE PLATE	MAR scanner 300 mm plate	OSMIC BLUE MIRRORS	2013-04-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	0.9794	CLSI	08ID-1

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	1.95	25	98.7	0.092	9	4.1		94048

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	1.95	2.02	98.7		0.577		4.2	9294

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	4ODS	1.95	25	89318	4730	98.27	0.2139	0.2122	0.2453	RANDOM	38.843

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]
0.02		0.75	-0.71		0.37

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.599
r_dihedral_angle_4_deg	17.924
r_dihedral_angle_3_deg	16.794
r_dihedral_angle_1_deg	6.555
r_mcangle_it	3.441
r_mcbond_it	2.293
r_mcbond_other	2.293
r_angle_refined_deg	1.472
r_angle_other_deg	1.109
r_chiral_restr	0.109

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.599
r_dihedral_angle_4_deg	17.924
r_dihedral_angle_3_deg	16.794
r_dihedral_angle_1_deg	6.555
r_mcangle_it	3.441
r_mcbond_it	2.293
r_mcbond_other	2.293
r_angle_refined_deg	1.472
r_angle_other_deg	1.109
r_chiral_restr	0.109
r_bond_refined_d	0.01
r_gen_planes_refined	0.006
r_bond_other_d	0.005
r_gen_planes_other	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9801
Nucleic Acid Atoms
Solvent Atoms	484
Heterogen Atoms	113

Software

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

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.