Experiment: 6VC9

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	0.1M sodium potassium phosphate pH 6.2, 35% 5-methyl-2,4-pentanediol, and 2.5% pentaerythritol ethoxylate

Crystal Properties
Matthews coefficient	Solvent content
3.02	59.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 118.31	α = 90
b = 74.22	β = 93.61
c = 148.326	γ = 90

Symmetry
Space Group	I 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	PIXEL	DECTRIS EIGER X 16M		2018-10-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)	0.976	PETRA III, EMBL c/o DESY	P14 (MX2)

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	2.25	59.038	99.2	0.071	0.082	0.998	11.15	3.851		60808			53.014

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	2.25	2.31	99.5		0.729	0.845	0.826	2.13	3.902

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	4H2I	2.25	30	58763	2017	99.51	0.238	0.2366	0.2785	RANDOM	60.829

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]
5.37		2.87	-3.4		-2.32

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.861
r_dihedral_angle_3_deg	18.523
r_dihedral_angle_4_deg	18.408
r_dihedral_angle_1_deg	9.001
r_angle_refined_deg	1.757
r_angle_other_deg	1.251
r_chiral_restr	0.077
r_bond_refined_d	0.016
r_gen_planes_refined	0.009
r_bond_other_d	0.005

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.861
r_dihedral_angle_3_deg	18.523
r_dihedral_angle_4_deg	18.408
r_dihedral_angle_1_deg	9.001
r_angle_refined_deg	1.757
r_angle_other_deg	1.251
r_chiral_restr	0.077
r_bond_refined_d	0.016
r_gen_planes_refined	0.009
r_bond_other_d	0.005
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5814
Nucleic Acid Atoms
Solvent Atoms	126
Heterogen Atoms	95

Software

Software
Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
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 R01GM133198.