Experiment: 6VUD

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1IS1	top 8 models from HHPred search: 4KDD_A, 1DD5_A, 1IS1_A, 5MLC_9, 1EH1_A, 4GFQ_A, 6ERI_Az, 1GE9_A
experimental model	PDB	6ERI	top 8 models from HHPred search: 4KDD_A, 1DD5_A, 1IS1_A, 5MLC_9, 1EH1_A, 4GFQ_A, 6ERI_Az, 1GE9_A
experimental model	PDB	1GE9	top 8 models from HHPred search: 4KDD_A, 1DD5_A, 1IS1_A, 5MLC_9, 1EH1_A, 4GFQ_A, 6ERI_Az, 1GE9_A
experimental model	PDB	4KDD	top 8 models from HHPred search: 4KDD_A, 1DD5_A, 1IS1_A, 5MLC_9, 1EH1_A, 4GFQ_A, 6ERI_Az, 1GE9_A
experimental model	PDB	4GFQ	top 8 models from HHPred search: 4KDD_A, 1DD5_A, 1IS1_A, 5MLC_9, 1EH1_A, 4GFQ_A, 6ERI_Az, 1GE9_A
experimental model	PDB	5MLC	top 8 models from HHPred search: 4KDD_A, 1DD5_A, 1IS1_A, 5MLC_9, 1EH1_A, 4GFQ_A, 6ERI_Az, 1GE9_A
experimental model	PDB	1DD5	top 8 models from HHPred search: 4KDD_A, 1DD5_A, 1IS1_A, 5MLC_9, 1EH1_A, 4GFQ_A, 6ERI_Az, 1GE9_A
experimental model	PDB	1EH1	top 8 models from HHPred search: 4KDD_A, 1DD5_A, 1IS1_A, 5MLC_9, 1EH1_A, 4GFQ_A, 6ERI_Az, 1GE9_A

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.2	290	RigakuReagents JCSG+ screen, condition C2: 20% (w/V) PEG 6000, 1000mM Lithium chloride, 100mM sodium citrate tribasic / citric acid pH 4.2 EhchA.00948.a.AE1.PS38617 at 13.45 mg/ml: cryo: 20% EG, tray 314079c2: puck wzi8-8

Crystal Properties
Matthews coefficient	Solvent content
2.97	58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.66	α = 90
b = 93.23	β = 109.728
c = 73.42	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	CCD	RAYONIX MX-300		2020-02-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

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	2.35	50	99.6	0.031	0.036	0.999	23.94	4.23		21055			68.698

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	2.35	2.41	99.9		0.575	0.656	0.882	2.95	4.279

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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	FREE R-VALUE	top 8 models from HHPred search: 4KDD_A, 1DD5_A, 1IS1_A, 5MLC_9, 1EH1_A, 4GFQ_A, 6ERI_Az, 1GE9_A	2.35	38.92	1.37	21030	1904	99.7	0.194	0.1898	0.2	0.2346	0.24	0	77.92

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	18.474
f_angle_d	0.6586
f_chiral_restr	0.043
f_bond_d	0.0057
f_plane_restr	0.0032

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2757
Nucleic Acid Atoms
Solvent Atoms	47
Heterogen Atoms	4

Software

Software
Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MR-Rosetta	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.