Experiment: 5DYL

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	293	10% PEG 5000 MME, 5% Tacsimate ph7.0, 0.1 M Hepes ph7, 15 mM spermidine, 25% glycerol

Crystal Properties
Matthews coefficient	Solvent content
3.95	68.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 192.471	α = 90
b = 117.773	β = 94.66
c = 67.682	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	CCD	MARMOSAIC 300 mm CCD		2013-07-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-B	0.97945	APS	23-ID-B

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	2.4	44.78	99.9	0.101	0.064	0.991	7.7	3.4		58714

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	2.4	2.47	99.9		0.907	0.574	0.654	1.5	3.4	4536

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2.4	44	55744	2967	99.86	0.2138	0.2121	0.2463	RANDOM	74.719

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]
0.82		0.24	-1.3		0.44

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.91
r_dihedral_angle_4_deg	15.757
r_dihedral_angle_3_deg	12.492
r_sphericity_bonded	6.55
r_dihedral_angle_1_deg	5.045
r_mcangle_it	2.158
r_rigid_bond_restr	1.957
r_mcbond_other	1.566
r_mcbond_it	1.565
r_angle_refined_deg	1.083

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.91
r_dihedral_angle_4_deg	15.757
r_dihedral_angle_3_deg	12.492
r_sphericity_bonded	6.55
r_dihedral_angle_1_deg	5.045
r_mcangle_it	2.158
r_rigid_bond_restr	1.957
r_mcbond_other	1.566
r_mcbond_it	1.565
r_angle_refined_deg	1.083
r_angle_other_deg	0.843
r_chiral_restr	0.063
r_bond_refined_d	0.007
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6237
Nucleic Acid Atoms
Solvent Atoms	124
Heterogen Atoms

Software

Software
Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
BALBES	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.