Experiment: 9T4D

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	5	289	Protein: 20mg/mL Precipitant condition: 29% PEG 6K, 0.1M NaOAc pH 5, 0.2M LiCl, 10mM MgCl2, 20mM NaF Ratio: 1:1

Crystal Properties
Matthews coefficient	Solvent content
2.9	58.8

Symmetry
Space Group	P 61

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		2024-04-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	0.97926	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	1.5	86.56	99.8	0.05	0.99	9.7	16.7		31754			22.9

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	1.5	1.53			1.55	0.25	0.4

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	1.5	86.559	31464	1506	98.856	0.164	0.1625	0.1624	0.1848	0.185	24.684

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]
-0.061	-0.031		-0.061		0.199

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.484
r_dihedral_angle_3_deg	13.793
r_lrange_it	9.803
r_lrange_other	9.018
r_dihedral_angle_2_deg	8.385
r_scangle_it	7.114
r_dihedral_angle_1_deg	6.741
r_scangle_other	6.645
r_scbond_it	4.628
r_scbond_other	4.237

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.484
r_dihedral_angle_3_deg	13.793
r_lrange_it	9.803
r_lrange_other	9.018
r_dihedral_angle_2_deg	8.385
r_scangle_it	7.114
r_dihedral_angle_1_deg	6.741
r_scangle_other	6.645
r_scbond_it	4.628
r_scbond_other	4.237
r_mcangle_it	3.901
r_mcangle_other	3.899
r_mcbond_it	2.657
r_mcbond_other	2.657
r_angle_refined_deg	1.963
r_angle_other_deg	0.716
r_symmetry_nbd_refined	0.271
r_nbd_refined	0.209
r_xyhbond_nbd_refined	0.202
r_symmetry_xyhbond_nbd_refined	0.199
r_symmetry_nbd_other	0.185
r_nbtor_refined	0.176
r_nbd_other	0.175
r_chiral_restr	0.099
r_symmetry_nbtor_other	0.086
r_metal_ion_refined	0.039
r_symmetry_xyhbond_nbd_other	0.017
r_bond_refined_d	0.011
r_gen_planes_refined	0.009
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1196
Nucleic Acid Atoms
Solvent Atoms	212
Heterogen Atoms	61

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.

9T4D | pdb_00009t4d