Experiment: 3Q9Y

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293	30% PEG 4000, 0.2M lithium sulfate, 0.1M TrisHCl, pH 8.5, vapor diffusion, sitting drop, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
1.98	37.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.664	α = 90
b = 45.91	β = 111.89
c = 63.628	γ = 90

Symmetry
Space Group	P 1 21 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	CCD	MAR CCD 165 mm		2008-09-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 5.2R	1.2	ELETTRA	5.2R

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	1.78	54.47	91.2	0.091	0.091	12.7	3.5	27533	27533

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.78	1.88	62.4		0.5	0.5	0.609	0.342	1.3	2.9	2727

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	PDB ENTRY 2PVR	1.8	35.1	27519	1406	94.37	0.1867	0.1838	0.2409	RANDOM	24.3087

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]
-0.71		0.41	0.48		0.54

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.995
r_dihedral_angle_4_deg	22.316
r_dihedral_angle_3_deg	16.538
r_dihedral_angle_1_deg	6.283
r_scangle_it	4.273
r_scbond_it	2.965
r_angle_refined_deg	1.867
r_mcangle_it	1.799
r_mcbond_it	1.15
r_chiral_restr	0.136

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.995
r_dihedral_angle_4_deg	22.316
r_dihedral_angle_3_deg	16.538
r_dihedral_angle_1_deg	6.283
r_scangle_it	4.273
r_scbond_it	2.965
r_angle_refined_deg	1.867
r_mcangle_it	1.799
r_mcbond_it	1.15
r_chiral_restr	0.136
r_bond_refined_d	0.024
r_gen_planes_refined	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2765
Nucleic Acid Atoms
Solvent Atoms	224
Heterogen Atoms	35

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
PHASER	phasing

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.