Experiment: 9QNK

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3IQU

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	0.095 M HEPES pH=7.1-7.7 0.19 M CaCl2 5% glycerol 24-29% PEG400

Crystal Properties
Matthews coefficient	Solvent content
2.68	54.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.915	α = 90
b = 113.043	β = 90
c = 63.168	γ = 90

Symmetry
Space Group	C 2 2 21

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 EIGER2 X 9M		2024-06-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.873128	ESRF	ID23-2

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	1.6	45.96	86.5	0.999	14.6	12.3		34194

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	1.6	1.63			0.777	2.4

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.6	45.96	32431	1739	86.52	0.16939	0.16801	0.1906	0.19581	0.2137	RANDOM	23.704

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]
0.47			-0.12		-0.35

RMS Deviations
Key	Refinement Restraint Deviation
r_scbond_it	15.515
r_scbond_other	14.812
r_long_range_B_other	14.751
r_long_range_B_refined	14.622
r_scangle_other	14.474
r_dihedral_angle_3_deg	14.465
r_mcbond_it	11.087
r_mcbond_other	10.668
r_mcangle_other	9.759
r_mcangle_it	9.742

RMS Deviations
Key	Refinement Restraint Deviation
r_scbond_it	15.515
r_scbond_other	14.812
r_long_range_B_other	14.751
r_long_range_B_refined	14.622
r_scangle_other	14.474
r_dihedral_angle_3_deg	14.465
r_mcbond_it	11.087
r_mcbond_other	10.668
r_mcangle_other	9.759
r_mcangle_it	9.742
r_dihedral_angle_1_deg	5.342
r_angle_refined_deg	1.367
r_angle_other_deg	0.524
r_chiral_restr	0.068
r_bond_refined_d	0.015
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1928
Nucleic Acid Atoms
Solvent Atoms	184
Heterogen Atoms	4

Software

Software
Software Name	Purpose
PDB-REDO	refinement
autoPROC	data reduction
Aimless	data scaling
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 R01GM157729.