Experiment: 8B2P

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5FYF

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.5	289	0.1 M HEPES pH 7.5 12% (w/v) polyethylene glycol 3350 10 mM octanoic acid

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.661	α = 90
b = 76.817	β = 90.53
c = 107.344	γ = 90

Symmetry
Space Group	P 1 21 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 6M		2018-10-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9763	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim 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	1.95	46.11	97.8	0.129	0.154	0.083	0.995	7.2	3.4		66934

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	1.95	2	97		1.365	1.615	0.857	0.519		3.5

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 (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	THROUGHOUT	5FYF	1.95	46.11	63554	3379	97.81	0.2311	0.229	0.23	0.2707	0.27	RANDOM	40.926

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]
5.17		3.75	-2.65		-2.59

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.019
r_dihedral_angle_3_deg	14.847
r_dihedral_angle_4_deg	14.64
r_dihedral_angle_1_deg	6.333
r_angle_refined_deg	1.256
r_angle_other_deg	1.12
r_chiral_restr	0.051
r_bond_other_d	0.005
r_bond_refined_d	0.004
r_gen_planes_refined	0.004

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.019
r_dihedral_angle_3_deg	14.847
r_dihedral_angle_4_deg	14.64
r_dihedral_angle_1_deg	6.333
r_angle_refined_deg	1.256
r_angle_other_deg	1.12
r_chiral_restr	0.051
r_bond_other_d	0.005
r_bond_refined_d	0.004
r_gen_planes_refined	0.004
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6843
Nucleic Acid Atoms
Solvent Atoms	285
Heterogen Atoms	106

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
autoPROC	data reduction

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.