Experiment: 9UJB

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1DY6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	20% PEG 4000, 0.2M lithium chloride

Crystal Properties
Matthews coefficient	Solvent content
2.02	39.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.503	α = 90
b = 51.362	β = 93.056
c = 131.086	γ = 90

Symmetry
Space Group	P 1 21 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	RIGAKU HyPix-6000HE		2024-06-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.54

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	2.1	25.68	99.9	0.996	13	7.3		28581

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	2.1	2.16			0.871

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	2.1	25.68	28567	1340	99.909	0.189	0.187	0.1879	0.2331	0.2352	17.648

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]
1.666		-0.722	-0.509		-1.074

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.419
r_dihedral_angle_6_deg	14.583
r_dihedral_angle_2_deg	13.401
r_dihedral_angle_1_deg	6.895
r_lrange_it	6.028
r_scangle_it	4.123
r_scbond_it	2.62
r_mcangle_it	2.209
r_angle_refined_deg	1.898
r_mcbond_it	1.389

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.419
r_dihedral_angle_6_deg	14.583
r_dihedral_angle_2_deg	13.401
r_dihedral_angle_1_deg	6.895
r_lrange_it	6.028
r_scangle_it	4.123
r_scbond_it	2.62
r_mcangle_it	2.209
r_angle_refined_deg	1.898
r_mcbond_it	1.389
r_nbtor_refined	0.308
r_symmetry_nbd_refined	0.228
r_nbd_refined	0.226
r_symmetry_xyhbond_nbd_refined	0.212
r_xyhbond_nbd_refined	0.196
r_chiral_restr	0.123
r_bond_refined_d	0.007
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4108
Nucleic Acid Atoms
Solvent Atoms	183
Heterogen Atoms	71

Software

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