Experiment: 7PBI

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	0.2 M NaCl and 2.2 M (NH4)2SO4.

Crystal Properties
Matthews coefficient	Solvent content
2.46	49.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.586	α = 90
b = 228.209	β = 90
c = 300.824	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	PIXEL	DECTRIS PILATUS 2M-F		2020-10-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	1.000041	SLS	X06DA

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	2.8	49.14	99.9	0.192	0.295	0.113	0.99	7.4	6.8		115793

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	2.8	2.85	99.9		1.887	2.046	0.785	0.41		6.7

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	7PBG	2.8	49.14	109803	5889	99.89	0.2106	0.2076	0.2654	RANDOM	51.923

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]
-1.3			4.01		-2.71

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.845
r_dihedral_angle_4_deg	21.278
r_dihedral_angle_3_deg	17.023
r_dihedral_angle_1_deg	7.037
r_angle_refined_deg	1.463
r_angle_other_deg	1.304
r_chiral_restr	0.065
r_bond_refined_d	0.006
r_gen_planes_refined	0.005
r_bond_other_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.845
r_dihedral_angle_4_deg	21.278
r_dihedral_angle_3_deg	17.023
r_dihedral_angle_1_deg	7.037
r_angle_refined_deg	1.463
r_angle_other_deg	1.304
r_chiral_restr	0.065
r_bond_refined_d	0.006
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	32848
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	496

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PDB_EXTRACT	data extraction
PHASER	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.