9TXV | pdb_00009txv

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	PDB_00007OJO

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	277	22% (w/v) PEG 3350, 0.2 M lithium sulfate, 0.1 M Tris, 1% (v/v) DMSO, 1 mM inhibitor

Crystal Properties
Matthews coefficient	Solvent content
2.41	48.9

Symmetry
Space Group	P 21 21 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 PILATUS3 6M		2023-09-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-1	0.96546	ESRF	MASSIF-1

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	2.9	41.66	99.8	0.403	0.409	0.995	12.81	37.6		11149			41.2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.9	2.98	99.8		2.375	2.421	0.772	1.89	26.9

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.9	41.66	11149	1114	99.749	0.204	0.1977	0.2019	0.2557	0.2532	Random selection	46.905

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]
2.786			1.956		-4.742

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.238
r_dihedral_angle_6_deg	13.972
r_lrange_it	8.855
r_lrange_other	8.853
r_dihedral_angle_1_deg	7.192
r_scangle_it	6.567
r_scangle_other	6.565
r_dihedral_angle_2_deg	6.534
r_mcangle_other	6.178
r_mcangle_it	6.177

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.238
r_dihedral_angle_6_deg	13.972
r_lrange_it	8.855
r_lrange_other	8.853
r_dihedral_angle_1_deg	7.192
r_scangle_it	6.567
r_scangle_other	6.565
r_dihedral_angle_2_deg	6.534
r_mcangle_other	6.178
r_mcangle_it	6.177
r_scbond_it	4.125
r_scbond_other	4.124
r_mcbond_it	3.826
r_mcbond_other	3.823
r_angle_refined_deg	1.481
r_chiral_restr_other	1.303
r_angle_other_deg	0.66
r_nbd_other	0.227
r_nbd_refined	0.209
r_symmetry_nbd_other	0.189
r_nbtor_refined	0.189
r_symmetry_xyhbond_nbd_refined	0.179
r_symmetry_nbd_refined	0.166
r_xyhbond_nbd_refined	0.142
r_ncsr_local_group_1	0.087
r_symmetry_nbtor_other	0.083
r_chiral_restr	0.066
r_ncsr_local_group_2	0.013
r_ncsr_local_group_3	0.009
r_gen_planes_refined	0.007
r_bond_refined_d	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3222
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	97

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.