Experiment: 9PD2

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3WUZ
experimental model	Other		internal Fab crystal structure

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		298	0.1 M CAPS pH 10.5, 20% PEG 8000, 0.2 M NaCl

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 37.854	α = 90
b = 46.753	β = 90
c = 335.052	γ = 90

Symmetry
Space Group	P 21 21 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 EIGER X 16M		2025-06-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL12-1	0.97946	SSRL	BL12-1

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	2.579	46.347	92.3	0.986	5.2	2.6		18280

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	2.58	2.72	86.6		0.301

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	2.579	46.347	18146	888	91.443	0.229	0.2261	0.2271	0.2774	0.2767	55.522

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]
-1.141			1.463		-0.323

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.329
r_dihedral_angle_6_deg	14.377
r_dihedral_angle_2_deg	10.513
r_lrange_it	8.712
r_dihedral_angle_1_deg	7.324
r_scangle_it	5.385
r_mcangle_it	4.177
r_scbond_it	3.494
r_mcbond_it	2.551
r_angle_refined_deg	1.594

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.329
r_dihedral_angle_6_deg	14.377
r_dihedral_angle_2_deg	10.513
r_lrange_it	8.712
r_dihedral_angle_1_deg	7.324
r_scangle_it	5.385
r_mcangle_it	4.177
r_scbond_it	3.494
r_mcbond_it	2.551
r_angle_refined_deg	1.594
r_nbtor_refined	0.304
r_symmetry_xyhbond_nbd_refined	0.269
r_symmetry_nbd_refined	0.239
r_nbd_refined	0.197
r_xyhbond_nbd_refined	0.127
r_chiral_restr	0.098
r_bond_refined_d	0.006
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4315
Nucleic Acid Atoms
Solvent Atoms	27
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.