23UB | pdb_000023ub

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6K58

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH MODE		293	100 mM Tris-HCl 120 mM MgCl2 17% w/v PEG8000 0.5 mM 2-(undecylcarbamoyl)benzoic acid

Crystal Properties
Matthews coefficient	Solvent content
2.75	55.23

Symmetry
Space Group	P 21 21 21

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 PILATUS3 X 6M		2025-04-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL45XU	1.000	SPring-8	BL45XU

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.63	46.4	100	0.193	0.997	11.6	13.3		143659			14.67

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	1.63	1.66			0.748

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	THROUGHOUT	6K58	1.63	46.4	143557	7312	99.969	0.19	0.1883	0.1882	0.2159	0.2157	22.111

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]
-0.071			0.516		-0.446

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.197
r_dihedral_angle_3_deg	12.781
r_dihedral_angle_2_deg	7.524
r_dihedral_angle_1_deg	6.811
r_lrange_it	5.923
r_lrange_other	5.893
r_scangle_it	4.656
r_scangle_other	4.655
r_mcangle_other	3.268
r_mcangle_it	3.267

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.197
r_dihedral_angle_3_deg	12.781
r_dihedral_angle_2_deg	7.524
r_dihedral_angle_1_deg	6.811
r_lrange_it	5.923
r_lrange_other	5.893
r_scangle_it	4.656
r_scangle_other	4.655
r_mcangle_other	3.268
r_mcangle_it	3.267
r_scbond_it	3.004
r_scbond_other	3.004
r_mcbond_it	2.246
r_mcbond_other	2.245
r_angle_refined_deg	1.897
r_dihedral_angle_other_2_deg	1.07
r_angle_other_deg	0.666
r_symmetry_nbd_refined	0.488
r_symmetry_xyhbond_nbd_refined	0.347
r_nbd_refined	0.236
r_symmetry_nbd_other	0.19
r_nbtor_refined	0.183
r_xyhbond_nbd_refined	0.166
r_symmetry_xyhbond_nbd_other	0.15
r_nbd_other	0.141
r_chiral_restr	0.096
r_symmetry_nbtor_other	0.076
r_metal_ion_refined	0.015
r_bond_refined_d	0.01
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7342
Nucleic Acid Atoms
Solvent Atoms	581
Heterogen Atoms	132

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.