Experiment: 9C20

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2VK5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	0.1M HEPES pH 7.5, 2.0M (NH4)2S04

Crystal Properties
Matthews coefficient	Solvent content
3.92	68.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 171.037	α = 90
b = 171.037	β = 90
c = 93.296	γ = 120

Symmetry
Space Group	P 64 2 2

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 200K		2022-01-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.54

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	2.1	24.81	99.14	0.935	16.7	5.3		47174

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.1			0.787

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.699	24.808	22433	1156	99.143	0.187	0.1838	0.2537	34.876

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]
0.349	0.175		0.349		-1.133

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.917
r_dihedral_angle_3_deg	14.424
r_dihedral_angle_1_deg	7.784
r_lrange_it	7.643
r_scangle_it	5.999
r_mcangle_it	5.09
r_scbond_it	3.916
r_dihedral_angle_2_deg	3.358
r_mcbond_it	3.272
r_angle_refined_deg	1.585

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.917
r_dihedral_angle_3_deg	14.424
r_dihedral_angle_1_deg	7.784
r_lrange_it	7.643
r_scangle_it	5.999
r_mcangle_it	5.09
r_scbond_it	3.916
r_dihedral_angle_2_deg	3.358
r_mcbond_it	3.272
r_angle_refined_deg	1.585
r_nbtor_refined	0.315
r_nbd_refined	0.225
r_symmetry_xyhbond_nbd_refined	0.196
r_symmetry_nbd_refined	0.167
r_xyhbond_nbd_refined	0.159
r_chiral_restr	0.11
r_gen_planes_refined	0.007
r_bond_refined_d	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3456
Nucleic Acid Atoms
Solvent Atoms	208
Heterogen Atoms	28

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
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 R01GM133198.