Experiment: 8Q60

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1PUY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	PEG 200, MES, magnesium chloride

Crystal Properties
Matthews coefficient	Solvent content
2.04	59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 26.517	α = 105.616
b = 30.04	β = 105.767
c = 45.224	γ = 94.343

Symmetry
Space Group	P -1

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 16M	Toroidal mirror	2023-03-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)	0.97625	PETRA III, EMBL c/o DESY	P14 (MX2)

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	2.5	28.56	0.9	0.03446	0.04873	0.998	13.98	2		3985			49.79

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.5	2.59	89		0.1918	0.2712	0.901	5.53	2

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-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.5	28.56	3985	382	90.179	0.283	0.2832	0.2782	0.2762	0.3279	0.328	34.254

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]
-2.019	5.863	-2.551	12.265	-4.386	-10.245

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	9.472
r_scangle_it	5.944
r_scbond_it	4.54
r_angle_refined_deg	1.96
r_nbtor_refined	0.334
r_xyhbond_nbd_refined	0.271
r_nbd_refined	0.233
r_symmetry_xyhbond_nbd_refined	0.189
r_symmetry_nbd_refined	0.173
r_metal_ion_refined	0.16

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	9.472
r_scangle_it	5.944
r_scbond_it	4.54
r_angle_refined_deg	1.96
r_nbtor_refined	0.334
r_xyhbond_nbd_refined	0.271
r_nbd_refined	0.233
r_symmetry_xyhbond_nbd_refined	0.189
r_symmetry_nbd_refined	0.173
r_metal_ion_refined	0.16
r_chiral_restr	0.085
r_gen_planes_refined	0.014
r_bond_refined_d	0.013

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	401
Solvent Atoms	175
Heterogen Atoms	163

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
autoPROC	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.