Experiment: 3LYQ

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	277	5% (w/w) PEG 3350, 7% isopropanol, 10mM FeCl3, 100mM trisodium citrate/citric acid pH 5.5, 10mM NaCl, vapor diffusion, hanging drop, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.29	62.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 114.08	α = 90
b = 114.08	β = 90
c = 88.77	γ = 90

Symmetry
Space Group	P 4 21 2

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	MARRESEARCH		2008-09-21	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	MARRESEARCH		2009-11-25	M	SINGLE WAVELENGTH
1,2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.900	ESRF	ID23-1
2	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.979	ESRF	ID23-1

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
1,2	2.3	22.88	95.4	0.056	33.35	18.2		25363		-3	49.2

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)
1,2	2.3	2.36	63		0.675	2.6	6.4	1205

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2.3	22.88	-3	24089	1267	95.6	0.232	0.229	0.23	0.292	0.29	RANDOM	45.838

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]
-0.34			-0.34		0.68

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.742
r_dihedral_angle_4_deg	19.853
r_dihedral_angle_3_deg	19.363
r_dihedral_angle_1_deg	5.612
r_scangle_it	3.825
r_scbond_it	2.249
r_angle_refined_deg	1.694
r_mcangle_it	1.576
r_mcbond_it	0.825
r_chiral_restr	0.164

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.742
r_dihedral_angle_4_deg	19.853
r_dihedral_angle_3_deg	19.363
r_dihedral_angle_1_deg	5.612
r_scangle_it	3.825
r_scbond_it	2.249
r_angle_refined_deg	1.694
r_mcangle_it	1.576
r_mcbond_it	0.825
r_chiral_restr	0.164
r_bond_refined_d	0.014
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2957
Nucleic Acid Atoms
Solvent Atoms	106
Heterogen Atoms	45

Software

Software
Software Name	Purpose
XSCALE	data scaling
SHELX	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
DNA	data collection
XDS	data reduction
SHELXD	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.