Experiment: 9N34

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2R6S

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		295	0.1 M MES monohydrate pH 6.5, 1.6 M Magnesium sulfate heptahydrate

Crystal Properties
Matthews coefficient	Solvent content
3.29	62.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 124.656	α = 90
b = 124.656	β = 90
c = 126.553	γ = 90

Symmetry
Space Group	P 4 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 EIGER2 XE CdTe 16M		2024-04-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX IV BEAMLINE BioMAX	0.976254	MAX IV	BioMAX

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim 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	2.86	126.55	97	0.392	0.407	0.108	0.992	11.5	26.3		23007

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.86	3.01	100		5.89	6.11	1.621	0.55	1.4	27.2

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-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.86	126.55	22976	1068	97.007	0.216	0.2144	0.2147	0.2524	0.2528	61.15

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]
0.982			0.982		-1.965

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	15.449
r_lrange_it	15.148
r_scangle_it	13.984
r_dihedral_angle_6_deg	13.676
r_dihedral_angle_3_deg	13.507
r_scbond_it	11.042
r_mcangle_it	10.554
r_mcbond_it	8.334
r_dihedral_angle_1_deg	5.706
r_angle_refined_deg	1.328

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	15.449
r_lrange_it	15.148
r_scangle_it	13.984
r_dihedral_angle_6_deg	13.676
r_dihedral_angle_3_deg	13.507
r_scbond_it	11.042
r_mcangle_it	10.554
r_mcbond_it	8.334
r_dihedral_angle_1_deg	5.706
r_angle_refined_deg	1.328
r_nbtor_refined	0.307
r_nbd_refined	0.215
r_symmetry_xyhbond_nbd_refined	0.201
r_symmetry_nbd_refined	0.19
r_xyhbond_nbd_refined	0.155
r_chiral_restr	0.06
r_bond_refined_d	0.009
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4628
Nucleic Acid Atoms
Solvent Atoms	26
Heterogen Atoms	2

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing
Coot	model building

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.