Experiment: 7BWY

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7BWX

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	0.1 M Bis-Tris pH 7.0, 4.0 M ammonium acetate

Crystal Properties
Matthews coefficient	Solvent content
4.09	69.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 92.311	α = 90
b = 92.311	β = 90
c = 222.669	γ = 120

Symmetry
Space Group	P 32 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 2M		2018-02-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-17A	0.9800	Photon Factory	BL-17A

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	2.02	46.16	99.9	0.082	0.085	1	21.1	19.8		72989

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.02	2.06	99.8		1.654	1.698	0.382	0.944	2.2	19.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	MOLECULAR REPLACEMENT	FREE R-VALUE	7BWX	2.02	45.725	72904	3649	99.874	0.181	0.1808	0.1789	0.18	0.2157	0.22	Random selection	56.926

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]
0.014	0.007		0.014		-0.046

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.863
r_dihedral_angle_3_deg	12.32
r_lrange_it	8.943
r_scangle_it	8.104
r_dihedral_angle_1_deg	7.912
r_scbond_it	7.257
r_mcangle_it	7.096
r_mcbond_it	5.842
r_dihedral_angle_4_deg	3.136
r_angle_refined_deg	2.081

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.863
r_dihedral_angle_3_deg	12.32
r_lrange_it	8.943
r_scangle_it	8.104
r_dihedral_angle_1_deg	7.912
r_scbond_it	7.257
r_mcangle_it	7.096
r_mcbond_it	5.842
r_dihedral_angle_4_deg	3.136
r_angle_refined_deg	2.081
r_nbtor_refined	0.327
r_symmetry_nbd_refined	0.276
r_nbd_refined	0.216
r_chiral_restr	0.144
r_xyhbond_nbd_refined	0.143
r_symmetry_xyhbond_nbd_refined	0.141
r_gen_planes_refined	0.012
r_bond_refined_d	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4239
Nucleic Acid Atoms
Solvent Atoms	318
Heterogen Atoms	24

Software

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