9XG0 | pdb_00009xg0

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7MLF

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2	38.51

Symmetry
Space Group	C 1 2 1

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 PILATUS 12M		2024-11-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL02U1	0.97918	SSRF	BL02U1

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	2.21	33.96	99.1	0.06	0.94	0.06	5.8		13407

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	2.21	2.27			0.5	3.5

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	FREE R-VALUE	7MLF	2.21	31.682	13382	664	98.899	0.182	0.1778	0.1861	0.2587	0.2618	37.484

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]
1.312		-0.305	-0.709		-0.441

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.421
r_dihedral_angle_3_deg	15.909
r_dihedral_angle_4_deg	13.923
r_dihedral_angle_1_deg	9.721
r_lrange_it	9.018
r_lrange_other	9.006
r_dihedral_angle_other_3_deg	6.49
r_scangle_it	6.365
r_scangle_other	6.363
r_mcangle_it	4.91

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.421
r_dihedral_angle_3_deg	15.909
r_dihedral_angle_4_deg	13.923
r_dihedral_angle_1_deg	9.721
r_lrange_it	9.018
r_lrange_other	9.006
r_dihedral_angle_other_3_deg	6.49
r_scangle_it	6.365
r_scangle_other	6.363
r_mcangle_it	4.91
r_mcangle_other	4.909
r_scbond_it	4.337
r_scbond_other	4.336
r_mcbond_other	3.493
r_mcbond_it	3.492
r_angle_refined_deg	1.758
r_angle_other_deg	1.367
r_xyhbond_nbd_refined	0.239
r_nbd_other	0.234
r_symmetry_xyhbond_nbd_refined	0.225
r_nbd_refined	0.209
r_symmetry_nbd_other	0.196
r_nbtor_refined	0.175
r_symmetry_nbd_refined	0.161
r_symmetry_nbtor_other	0.08
r_chiral_restr	0.077
r_bond_refined_d	0.01
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2347
Nucleic Acid Atoms
Solvent Atoms	162
Heterogen Atoms	32

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.