Experiment: 9QYR

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6THT

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH		293	10 mM Tris, 150 mM NaCl, 0.6 M succinic acid, pH 7.0

Crystal Properties
Matthews coefficient	Solvent content
2.95	58.29

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 96.57	α = 90
b = 96.57	β = 90
c = 73.16	γ = 90

Symmetry
Space Group	P 41 21 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 PILATUS3 6M		2024-07-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, DESY BEAMLINE P11	1.000	PETRA III, DESY	P11

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	1.71	48.29	99.5	0.806	19.09	25.93		964320

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	1.71	1.81	97		0.806	1.06

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.71	48.285	37807	1891	99.636	0.173	0.1713	0.1713	0.2038	0.2039	30.692

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]
-0.408			-0.408		0.816

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.711
r_dihedral_angle_3_deg	11.123
r_dihedral_angle_2_deg	8.164
r_lrange_it	7.096
r_dihedral_angle_1_deg	7.013
r_scangle_it	4.984
r_scbond_it	3.938
r_mcangle_it	3.302
r_mcbond_it	2.671
r_angle_refined_deg	1.98

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.711
r_dihedral_angle_3_deg	11.123
r_dihedral_angle_2_deg	8.164
r_lrange_it	7.096
r_dihedral_angle_1_deg	7.013
r_scangle_it	4.984
r_scbond_it	3.938
r_mcangle_it	3.302
r_mcbond_it	2.671
r_angle_refined_deg	1.98
r_symmetry_nbd_refined	0.369
r_symmetry_xyhbond_nbd_refined	0.355
r_nbtor_refined	0.316
r_xyhbond_nbd_refined	0.221
r_nbd_refined	0.215
r_chiral_restr	0.135
r_bond_refined_d	0.011
r_gen_planes_refined	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1943
Nucleic Acid Atoms
Solvent Atoms	292
Heterogen Atoms	2

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	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 R01GM157729.