9VTL | pdb_00009vtl

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7K3T

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		289.15	0.1 M Bis-Tris pH6.5, 30% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.7	54.37

Symmetry
Space Group	I 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 PILATUS3 R 200K-A		2025-06-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.54178

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	1.97	29.09	99	0.153	0.189	0.109	0.964	4.9	2.9		25381

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	2.2	2.27	99.1		0.369		2.9

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	1.97	24.288	25381	1242	98.548	0.219	0.2162	0.2146	0.2653	0.2577	26.881

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]
-1.291		0.126	0.724		0.519

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.65
r_dihedral_angle_6_deg	14.072
r_dihedral_angle_2_deg	10.778
r_lrange_it	9.659
r_lrange_other	9.53
r_dihedral_angle_1_deg	7.62
r_scangle_it	5.851
r_scangle_other	5.85
r_mcangle_it	3.942
r_mcangle_other	3.942

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.65
r_dihedral_angle_6_deg	14.072
r_dihedral_angle_2_deg	10.778
r_lrange_it	9.659
r_lrange_other	9.53
r_dihedral_angle_1_deg	7.62
r_scangle_it	5.851
r_scangle_other	5.85
r_mcangle_it	3.942
r_mcangle_other	3.942
r_scbond_it	3.646
r_scbond_other	3.631
r_mcbond_it	2.506
r_mcbond_other	2.503
r_angle_refined_deg	1.833
r_angle_other_deg	0.609
r_xyhbond_nbd_refined	0.28
r_symmetry_xyhbond_nbd_refined	0.271
r_nbd_refined	0.222
r_symmetry_nbd_other	0.204
r_nbd_other	0.202
r_nbtor_refined	0.189
r_symmetry_nbd_refined	0.127
r_symmetry_xyhbond_nbd_other	0.118
r_symmetry_nbtor_other	0.091
r_chiral_restr	0.085
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2323
Nucleic Acid Atoms
Solvent Atoms	376
Heterogen Atoms	34

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.