Experiment: 9QYP

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
3.83	67.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 97.91	α = 90
b = 101.87	β = 90
c = 265.81	γ = 90

Symmetry
Space Group	I 2 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 6M		2023-02-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, DESY BEAMLINE P11	1.0000	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	2.007	48.955	100	0.998	7.98	10.34		919234

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	2.01	2.13			0.499

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	2.007	48.955	88905	4446	99.926	0.21	0.2079	0.2079	0.2498	0.25	46.189

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]
0.819			3.45		-4.269

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.232
r_dihedral_angle_6_deg	14.212
r_dihedral_angle_2_deg	9.471
r_lrange_it	9.389
r_dihedral_angle_1_deg	7.8
r_scangle_it	7.129
r_mcangle_it	6.216
r_scbond_it	5.319
r_mcbond_it	4.319
r_angle_refined_deg	1.912

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.232
r_dihedral_angle_6_deg	14.212
r_dihedral_angle_2_deg	9.471
r_lrange_it	9.389
r_dihedral_angle_1_deg	7.8
r_scangle_it	7.129
r_mcangle_it	6.216
r_scbond_it	5.319
r_mcbond_it	4.319
r_angle_refined_deg	1.912
r_nbtor_refined	0.316
r_nbd_refined	0.225
r_xyhbond_nbd_refined	0.189
r_symmetry_xyhbond_nbd_refined	0.157
r_symmetry_nbd_refined	0.146
r_chiral_restr	0.115
r_bond_refined_d	0.007
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5870
Nucleic Acid Atoms
Solvent Atoms	332
Heterogen Atoms

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.