9RGU | pdb_00009rgu

X-RAY DIFFRACTION

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

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.5	298	100mM Tris, pH 7.5, 2.1M (NH4)2SO4, 10% octanol

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.58

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 EIGER2 XE CdTe 16M		2024-10-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX IV BEAMLINE BioMAX	0.7290	MAX IV	BioMAX

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.7	47.9	100	0.037	0.999	14	13.6		192681

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	1.7	1.73			0.34	1.2

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	1.7	47.9	192522	9602	99.927	0.219	0.217	0.2159	0.2476	0.2436	35.33

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]
-0.196			2.677		-2.48

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.179
r_dihedral_angle_4_deg	14.349
r_dihedral_angle_3_deg	13.491
r_dihedral_angle_1_deg	5.752
r_lrange_it	5.466
r_scangle_it	3.14
r_mcangle_it	2.152
r_scbond_it	1.893
r_mcbond_it	1.322
r_angle_refined_deg	0.949

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.179
r_dihedral_angle_4_deg	14.349
r_dihedral_angle_3_deg	13.491
r_dihedral_angle_1_deg	5.752
r_lrange_it	5.466
r_scangle_it	3.14
r_mcangle_it	2.152
r_scbond_it	1.893
r_mcbond_it	1.322
r_angle_refined_deg	0.949
r_nbtor_refined	0.303
r_nbd_refined	0.186
r_symmetry_nbd_refined	0.159
r_xyhbond_nbd_refined	0.14
r_symmetry_xyhbond_nbd_refined	0.106
r_chiral_restr	0.073
r_bond_refined_d	0.003
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11571
Nucleic Acid Atoms
Solvent Atoms	490
Heterogen Atoms	308

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.