Experiment: 7VGB

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3MUN

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.2M Trimethylamine N-oxide dihydrate, 0.1M Tris pH 8.5, 20% (w/v) Polyethylene glycol monomethyl ether 2000

Crystal Properties
Matthews coefficient	Solvent content
2.19	43.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.39	α = 90
b = 125.395	β = 96.837
c = 89.848	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		2020-06-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL18U1	0.979	SSRF	BL18U1

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	2.227	44.198	99.86	0.1398	0.1516	0.0581	0.994	12.53	6.8		64538			19.9

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	2.227	2.31	99.97		0.5265	0.5753	0.2292	0.899	4.37	6.3

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-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3MUN	2.227	44.198	64531	3237	99.744	0.155	0.1524	0.15	0.2072	0.21	21.548

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]
1.048		-1.486	-0.767		0.073

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.3
r_dihedral_angle_4_deg	17.429
r_dihedral_angle_3_deg	14.65
r_dihedral_angle_1_deg	7.209
r_lrange_it	5.373
r_scangle_it	3.582
r_mcangle_it	2.451
r_scbond_it	2.315
r_mcbond_it	1.547
r_angle_refined_deg	1.43

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.3
r_dihedral_angle_4_deg	17.429
r_dihedral_angle_3_deg	14.65
r_dihedral_angle_1_deg	7.209
r_lrange_it	5.373
r_scangle_it	3.582
r_mcangle_it	2.451
r_scbond_it	2.315
r_mcbond_it	1.547
r_angle_refined_deg	1.43
r_nbtor_refined	0.313
r_symmetry_nbd_refined	0.203
r_nbd_refined	0.202
r_symmetry_xyhbond_nbd_refined	0.171
r_xyhbond_nbd_refined	0.148
r_chiral_restr	0.111
r_bond_refined_d	0.007
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10892
Nucleic Acid Atoms
Solvent Atoms	1016
Heterogen Atoms	105

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	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.