Experiment: 8FAQ

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	291.15	50% PEG-200, 0.1M citrate pH 5.5, final pH 6.9

Crystal Properties
Matthews coefficient	Solvent content
3.39	63.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 99.705	α = 90
b = 99.705	β = 90
c = 395.31	γ = 120

Symmetry
Space Group	H 3 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 EIGER X 9M		2021-12-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	1.12723	APS	21-ID-D

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	2.035	79.252	98.6	0.077	0.079	0.999	21.6	20.4		48446

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.035	2.071	98		1.642	0.865	2.2

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	NONE	2YP4	2.035	79.252	48446	2400	98.556	0.204	0.2028	0.2291	54.981

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]
-0.005	-0.003		-0.005		0.016

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.247
r_dihedral_angle_3_deg	15.356
r_dihedral_angle_4_deg	14.224
r_lrange_it	8.29
r_scangle_it	6.968
r_dihedral_angle_1_deg	6.933
r_scbond_it	5.072
r_mcangle_it	4.935
r_mcbond_it	3.901
r_angle_refined_deg	1.473

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.247
r_dihedral_angle_3_deg	15.356
r_dihedral_angle_4_deg	14.224
r_lrange_it	8.29
r_scangle_it	6.968
r_dihedral_angle_1_deg	6.933
r_scbond_it	5.072
r_mcangle_it	4.935
r_mcbond_it	3.901
r_angle_refined_deg	1.473
r_nbtor_refined	0.313
r_nbd_refined	0.215
r_symmetry_nbd_refined	0.187
r_symmetry_xyhbond_nbd_refined	0.15
r_xyhbond_nbd_refined	0.144
r_chiral_restr	0.103
r_bond_refined_d	0.007
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3941
Nucleic Acid Atoms
Solvent Atoms	139
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
XDS	data scaling
PHENIX	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.