Experiment: 7YBD

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		293	0.1 M HEPES-NaOH pH 7.5, 0.2 M magnesium formate, and 18% PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.35	47.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.899	α = 90
b = 65.233	β = 118.105
c = 81.994	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	PIXEL	DECTRIS PILATUS3 S 6M		2021-11-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-5A	1	Photon Factory	BL-5A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	2.13	48.68	98.7	0.066	0.079	0.997	11.9	3.4		21383

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.13	2.19	98.2		0.608	0.718	0.769	2.2	3.5

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-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.13	41.452	21382	1095	98.453	0.182	0.1786	0.18	0.2392	0.24	44.552

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]
0.133		0.015	0.083		-0.148

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.341
r_dihedral_angle_4_deg	22.969
r_dihedral_angle_3_deg	17.367
r_lrange_it	9.161
r_dihedral_angle_1_deg	7.456
r_scangle_it	7.397
r_scbond_it	4.863
r_mcangle_it	4.849
r_mcbond_it	3.323
r_angle_refined_deg	1.519

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.341
r_dihedral_angle_4_deg	22.969
r_dihedral_angle_3_deg	17.367
r_lrange_it	9.161
r_dihedral_angle_1_deg	7.456
r_scangle_it	7.397
r_scbond_it	4.863
r_mcangle_it	4.849
r_mcbond_it	3.323
r_angle_refined_deg	1.519
r_nbtor_refined	0.314
r_symmetry_nbd_refined	0.248
r_nbd_refined	0.234
r_symmetry_xyhbond_nbd_refined	0.216
r_xyhbond_nbd_refined	0.157
r_chiral_restr	0.119
r_gen_planes_refined	0.007
r_bond_refined_d	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2863
Nucleic Acid Atoms
Solvent Atoms	145
Heterogen Atoms	10

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	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.