Experiment: 9T4F

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	9T48

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	9	289	Protein: 20 mg/mL Precipitant condition: 25% w/v PEG 1500, 0.1M SPG pH 9 Ratio: 1:1

Crystal Properties
Matthews coefficient	Solvent content
2.4	49.1

Symmetry
Space Group	P 65 2 2

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 6M		2024-03-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	0.97918	ALBA	XALOC

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	1.321	51.348	98.8	0.01	1	34.3	37.1		37944			23.3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.321	1.344			0.3	0.87	2.2

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	1.426	51.32	30389	1551	99.22	0.188	0.1864	0.1955	0.2185	0.2336	26.567

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]
0.266	0.133		0.266		-0.862

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.204
r_dihedral_angle_3_deg	13.623
r_dihedral_angle_2_deg	11.212
r_lrange_other	8.2
r_lrange_it	8.194
r_dihedral_angle_1_deg	6.595
r_scangle_other	6.42
r_scangle_it	6.406
r_scbond_it	4.181
r_scbond_other	4.18

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.204
r_dihedral_angle_3_deg	13.623
r_dihedral_angle_2_deg	11.212
r_lrange_other	8.2
r_lrange_it	8.194
r_dihedral_angle_1_deg	6.595
r_scangle_other	6.42
r_scangle_it	6.406
r_scbond_it	4.181
r_scbond_other	4.18
r_mcangle_it	3.941
r_mcangle_other	3.939
r_mcbond_it	2.821
r_mcbond_other	2.821
r_angle_refined_deg	2.146
r_angle_other_deg	0.736
r_symmetry_xyhbond_nbd_refined	0.206
r_nbd_refined	0.204
r_xyhbond_nbd_refined	0.195
r_symmetry_nbd_other	0.193
r_nbtor_refined	0.179
r_symmetry_nbd_refined	0.176
r_nbd_other	0.168
r_chiral_restr	0.108
r_symmetry_nbtor_other	0.088
r_symmetry_xyhbond_nbd_other	0.05
r_bond_refined_d	0.012
r_gen_planes_refined	0.011
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1161
Nucleic Acid Atoms
Solvent Atoms	133
Heterogen Atoms	11

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.

9T4F | pdb_00009t4f