9T91 | pdb_00009t91

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	9T4Y

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	278	MES, ethylene glycol

Crystal Properties
Matthews coefficient	Solvent content
2.97	58.66

Symmetry
Space Group	P 31 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 EIGER X 16M		2024-08-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)	0.6888	PETRA III, EMBL c/o DESY	P13 (MX1)

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	1.6	43.33	99.6	0.079	0.081	0.018	0.999	19.4	20.5		43532			22.81

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.6	1.69	99.2		1.373	1.407	0.304	0.942	2.4	20.9

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	1.6	42.883	43510	2217	99.406	0.183	0.1817	0.1941	0.2017	0.2126	30.216

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]
1.309	0.655		1.309		-4.247

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.598
r_dihedral_angle_4_deg	15.008
r_dihedral_angle_3_deg	10.667
r_dihedral_angle_1_deg	7.381
r_lrange_it	5.815
r_lrange_other	5.801
r_scangle_it	4.914
r_scangle_other	4.912
r_scbond_it	3.464
r_scbond_other	3.463

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.598
r_dihedral_angle_4_deg	15.008
r_dihedral_angle_3_deg	10.667
r_dihedral_angle_1_deg	7.381
r_lrange_it	5.815
r_lrange_other	5.801
r_scangle_it	4.914
r_scangle_other	4.912
r_scbond_it	3.464
r_scbond_other	3.463
r_mcangle_it	2.938
r_mcangle_other	2.938
r_mcbond_other	2.256
r_mcbond_it	2.254
r_angle_refined_deg	1.82
r_angle_other_deg	1.445
r_nbd_refined	0.195
r_symmetry_nbd_other	0.174
r_nbtor_refined	0.17
r_nbd_other	0.163
r_symmetry_nbd_refined	0.154
r_xyhbond_nbd_refined	0.122
r_metal_ion_refined	0.107
r_symmetry_xyhbond_nbd_refined	0.105
r_chiral_restr	0.088
r_symmetry_nbtor_other	0.083
r_bond_refined_d	0.012
r_gen_planes_refined	0.011
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1882
Nucleic Acid Atoms
Solvent Atoms	177
Heterogen Atoms	87

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.