Experiment: 1Y82

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	modified microbatch	5.5	291	0.1M citrate, 0.1M sodium chloride, 0.1M lithium sulfate, 30% v/v PEG 400, pH 5.5, modified microbatch, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.601	α = 90
b = 103.667	β = 90
c = 104.253	γ = 90

Symmetry
Space Group	P 21 21 21

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 225 mm CCD			M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	mar165			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	0.97623	APS	22-ID
2	SYNCHROTRON	APS BEAMLINE 22-BM	0.97623	APS	22-BM

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	40	98.7	0.109				28211

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	2.38	99.7		0.349

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 (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAS	THROUGHOUT	2.3	73.521	28124	875	98.353	0.223	0.22346	0.2216	0.2779	THIN SHELLS	21.477

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]
1.792			-1.609		-0.183

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.406
r_dihedral_angle_4_deg	19.458
r_dihedral_angle_3_deg	15.827
r_dihedral_angle_1_deg	5.797
r_scangle_it	4.901
r_mcangle_it	4.089
r_scbond_it	3.434
r_mcbond_it	2.655
r_angle_refined_deg	1.381
r_nbtor_refined	0.302

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.406
r_dihedral_angle_4_deg	19.458
r_dihedral_angle_3_deg	15.827
r_dihedral_angle_1_deg	5.797
r_scangle_it	4.901
r_mcangle_it	4.089
r_scbond_it	3.434
r_mcbond_it	2.655
r_angle_refined_deg	1.381
r_nbtor_refined	0.302
r_nbd_refined	0.201
r_symmetry_vdw_refined	0.192
r_symmetry_hbond_refined	0.178
r_xyhbond_nbd_refined	0.145
r_chiral_restr	0.09
r_bond_refined_d	0.017
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4473
Nucleic Acid Atoms
Solvent Atoms	39
Heterogen Atoms	42

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
RESOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
ARP/wARP	model building

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.