Experiment: 1YB3

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	modified microbatch	3.6	291	12% w/v PEG 4000, 0.2M sodium chloride, 0.2M magnesium chloride, 0.1M sodium citrate, pH 3.6, modified microbatch, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.79	55.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 109.134	α = 90
b = 44.388	β = 118.82
c = 55.326	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			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	0.9795	APS	22-ID

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	1.6	50	84.8	0.052				26254

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	1.6	1.66	34.6		0.218

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	1.6	48.45	26254	1312	84.792	0.205	0.20521	0.2039	0.2291	RANDOM	26.965

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]
-1.491		-0.15	0.988		0.359

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.983
r_dihedral_angle_4_deg	17.644
r_dihedral_angle_3_deg	12.034
r_dihedral_angle_1_deg	5.31
r_scangle_it	3.637
r_mcangle_it	3.04
r_scbond_it	2.437
r_mcbond_it	2.373
r_angle_refined_deg	1.151
r_nbtor_refined	0.309

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.983
r_dihedral_angle_4_deg	17.644
r_dihedral_angle_3_deg	12.034
r_dihedral_angle_1_deg	5.31
r_scangle_it	3.637
r_mcangle_it	3.04
r_scbond_it	2.437
r_mcbond_it	2.373
r_angle_refined_deg	1.151
r_nbtor_refined	0.309
r_symmetry_vdw_refined	0.212
r_nbd_refined	0.194
r_symmetry_hbond_refined	0.118
r_xyhbond_nbd_refined	0.098
r_chiral_restr	0.087
r_bond_refined_d	0.012
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1392
Nucleic Acid Atoms
Solvent Atoms	102
Heterogen Atoms	1

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
RESOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
ISAS	phasing
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.