9RTH | pdb_00009rth

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4X1B

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	15% (w/v) PEG 3350, 16% (v/v) glycerol, 8 mM disodium malonate, 150 mM Na-PIPES pH 6.5

Crystal Properties
Matthews coefficient	Solvent content
3.82	67.82

Symmetry
Space Group	C 2 2 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 EIGER X 16M		2025-02-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 1	0.97946	SOLEIL	PROXIMA 1

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	2.52	74.32	90.4	0.992	9.1	11.5		26235

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	2.52	2.77			0.596

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	2.52	74.32	26235	1324	66.34	0.181	0.1767	0.1821	0.2598	0.2578	40.236

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]
-0.377			0.124		0.253

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.772
r_dihedral_angle_4_deg	20.327
r_dihedral_angle_3_deg	19.266
r_lrange_it	9.232
r_lrange_other	9.217
r_dihedral_angle_1_deg	7.862
r_scangle_it	6.403
r_scangle_other	6.395
r_mcangle_it	5.582
r_mcangle_other	5.581

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.772
r_dihedral_angle_4_deg	20.327
r_dihedral_angle_3_deg	19.266
r_lrange_it	9.232
r_lrange_other	9.217
r_dihedral_angle_1_deg	7.862
r_scangle_it	6.403
r_scangle_other	6.395
r_mcangle_it	5.582
r_mcangle_other	5.581
r_scbond_it	3.877
r_scbond_other	3.858
r_mcbond_it	3.469
r_mcbond_other	3.454
r_angle_refined_deg	1.645
r_angle_other_deg	1.305
r_nbd_refined	0.21
r_symmetry_nbd_other	0.195
r_nbtor_refined	0.172
r_xyhbond_nbd_refined	0.167
r_nbd_other	0.136
r_symmetry_xyhbond_nbd_refined	0.116
r_metal_ion_refined	0.091
r_symmetry_nbtor_other	0.082
r_symmetry_xyhbond_nbd_other	0.072
r_chiral_restr	0.071
r_symmetry_nbd_refined	0.057
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5045
Nucleic Acid Atoms
Solvent Atoms	327
Heterogen Atoms	22

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.