9TXU | pdb_00009txu

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
2.4	48.7

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	2.35	41.66	99.8	0.205	0.211	0.997	10.53	17.7		20593			43.7

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	2.35	2.41	99.8		1.098	1.145	0.837	1.86	12.2

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.35	41.66	20593	2055	99.796	0.214	0.2115	0.2179	0.2353	0.2377	Random selection	46.594

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]
2.903			0.239		-3.142

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	12.865
r_dihedral_angle_3_deg	12.811
r_lrange_other	9.003
r_lrange_it	9
r_dihedral_angle_2_deg	7.797
r_dihedral_angle_1_deg	6.556
r_scangle_it	5.784
r_scangle_other	5.783
r_mcangle_it	5.118
r_mcangle_other	5.117

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	12.865
r_dihedral_angle_3_deg	12.811
r_lrange_other	9.003
r_lrange_it	9
r_dihedral_angle_2_deg	7.797
r_dihedral_angle_1_deg	6.556
r_scangle_it	5.784
r_scangle_other	5.783
r_mcangle_it	5.118
r_mcangle_other	5.117
r_scbond_it	3.49
r_scbond_other	3.489
r_mcbond_it	3.111
r_mcbond_other	3.11
r_angle_refined_deg	1.349
r_angle_other_deg	0.592
r_nbd_refined	0.203
r_symmetry_nbd_other	0.187
r_nbtor_refined	0.183
r_symmetry_xyhbond_nbd_refined	0.165
r_nbd_other	0.163
r_chiral_restr_other	0.152
r_symmetry_nbd_refined	0.128
r_xyhbond_nbd_refined	0.124
r_ncsr_local_group_2	0.108
r_symmetry_nbtor_other	0.079
r_ncsr_local_group_1	0.076
r_chiral_restr	0.059
r_ncsr_local_group_3	0.018
r_bond_refined_d	0.005
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3236
Nucleic Acid Atoms
Solvent Atoms	83
Heterogen Atoms	99

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.