9RTF | pdb_00009rtf

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
3.9	68.47

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 EIGER2 S 16M		2025-03-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX IV BEAMLINE BioMAX	0.99987	MAX IV	BioMAX

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	2.16	104.01	92.8	0.985	6.2	8		47443

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	2.16	2.35			0.263

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	2.16	104.01	47442	2373	74.613	0.187	0.1846	0.1911	0.2321	0.2343	38.431

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]
-0.583			0.433		0.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.977
r_dihedral_angle_4_deg	20.09
r_dihedral_angle_3_deg	18.056
r_lrange_it	9.004
r_lrange_other	9
r_dihedral_angle_1_deg	7.348
r_scangle_it	6.476
r_scangle_other	6.475
r_mcangle_it	5.233
r_mcangle_other	5.233

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.977
r_dihedral_angle_4_deg	20.09
r_dihedral_angle_3_deg	18.056
r_lrange_it	9.004
r_lrange_other	9
r_dihedral_angle_1_deg	7.348
r_scangle_it	6.476
r_scangle_other	6.475
r_mcangle_it	5.233
r_mcangle_other	5.233
r_scbond_it	4.127
r_scbond_other	4.103
r_mcbond_it	3.378
r_mcbond_other	3.377
r_angle_refined_deg	1.63
r_angle_other_deg	1.321
r_nbd_refined	0.203
r_symmetry_nbd_refined	0.192
r_symmetry_nbd_other	0.187
r_nbtor_refined	0.168
r_nbd_other	0.168
r_xyhbond_nbd_refined	0.16
r_symmetry_xyhbond_nbd_refined	0.155
r_metal_ion_refined	0.144
r_symmetry_nbtor_other	0.083
r_chiral_restr	0.075
r_symmetry_xyhbond_nbd_other	0.015
r_bond_refined_d	0.01
r_gen_planes_refined	0.007
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5201
Nucleic Acid Atoms
Solvent Atoms	354
Heterogen Atoms	38

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.