Experiment: 5YWX

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	LIQUID DIFFUSION	8.5	293	35% PEG6000, 5 mM DTT, 2 mM MgCl2, 2 mM Glutathione, 2% Dioxane, 50 mM Tris-HCl, pH 8.5

Crystal Properties
Matthews coefficient	Solvent content
2.22	44.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.04	α = 98.97
b = 48.17	β = 92.34
c = 92.11	γ = 90.01

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 PILATUS3 S 6M		2014-03-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.97625	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	1.74	47.04	97.1	0.102	0.126	0.072	0.988	5.9	3		79469

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.74	1.77	95.6		0.609	0.748	0.429	0.643		3

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	2CVD	1.74	47.04	75464	3992	97.05	0.2055	0.203	0.2527	RANDOM	21.977

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]
-0.48	0.04	-0.09	0.54	0.01	-0.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.458
r_dihedral_angle_3_deg	13.881
r_dihedral_angle_4_deg	12.288
r_dihedral_angle_1_deg	5.779
r_angle_refined_deg	1.47
r_angle_other_deg	0.807
r_chiral_restr	0.081
r_bond_refined_d	0.011
r_gen_planes_refined	0.008
r_gen_planes_other	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.458
r_dihedral_angle_3_deg	13.881
r_dihedral_angle_4_deg	12.288
r_dihedral_angle_1_deg	5.779
r_angle_refined_deg	1.47
r_angle_other_deg	0.807
r_chiral_restr	0.081
r_bond_refined_d	0.011
r_gen_planes_refined	0.008
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6552
Nucleic Acid Atoms
Solvent Atoms	583
Heterogen Atoms	208

Software

Software
Software Name	Purpose
MOSFLM	data reduction
Aimless	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

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.