23UH | pdb_000023uh

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 magnesium chloride, 18% w/v PEG8000, 0.5 mM 2-(undecylcarbamoyl)benzoic acid Crystals were soaked in cryobuffer containing benzene.

Crystal Properties
Matthews coefficient	Solvent content
2.7	54.43

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	1.48	46.1	100	0.291	0.996	11.7	13.1		187855			9.52

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	1.48	1.51			0.823

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	1.48	46.1	187753	9377	99.928	0.178	0.1765	0.1738	0.199	0.1964	15.024

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]
-0.084			0.436		-0.351

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.145
r_dihedral_angle_3_deg	12.393
r_dihedral_angle_2_deg	7.866
r_dihedral_angle_1_deg	6.336
r_lrange_it	5.05
r_lrange_other	4.952
r_scangle_it	4.164
r_scangle_other	4.163
r_scbond_it	2.683
r_scbond_other	2.683

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.145
r_dihedral_angle_3_deg	12.393
r_dihedral_angle_2_deg	7.866
r_dihedral_angle_1_deg	6.336
r_lrange_it	5.05
r_lrange_other	4.952
r_scangle_it	4.164
r_scangle_other	4.163
r_scbond_it	2.683
r_scbond_other	2.683
r_mcangle_other	2.271
r_mcangle_it	2.27
r_angle_refined_deg	1.984
r_mcbond_it	1.532
r_mcbond_other	1.532
r_dihedral_angle_other_2_deg	1.108
r_angle_other_deg	0.677
r_nbd_refined	0.232
r_nbtor_refined	0.189
r_symmetry_nbd_other	0.185
r_nbd_other	0.146
r_xyhbond_nbd_refined	0.139
r_symmetry_nbd_refined	0.103
r_chiral_restr	0.102
r_symmetry_xyhbond_nbd_refined	0.088
r_symmetry_nbtor_other	0.078
r_bond_refined_d	0.011
r_gen_planes_refined	0.01
r_symmetry_xyhbond_nbd_other	0.004
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	816
Heterogen Atoms	144

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.