Experiment: 9T48

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6WOG

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5	289	Protein: 20mg/mL PCP-IP8: 10mM Precipitant condition: 20% PEG 6K, 0.1M NaOAc pH 5, 0.2M LiCl,10mM MgCl2 Ratio: 1:1

Crystal Properties
Matthews coefficient	Solvent content
2.6	53.2

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 PILATUS 6M		2022-05-05	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	78.42	100	0.03	0.999	13.8	12.2		28885			19.6

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			0.661	0.521	1.3

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	THROUGHOUT	1.5	50.075	28825	1444	99.965	0.177	0.1758	0.181	0.1954	0.1997	RANDOM	23.516

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]
-1.628			-1.089		2.717

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.476
r_dihedral_angle_3_deg	13.363
r_dihedral_angle_2_deg	9.586
r_lrange_it	7.657
r_lrange_other	7.459
r_dihedral_angle_1_deg	6.857
r_scangle_it	6.13
r_scangle_other	6.127
r_scbond_other	3.745
r_scbond_it	3.736

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.476
r_dihedral_angle_3_deg	13.363
r_dihedral_angle_2_deg	9.586
r_lrange_it	7.657
r_lrange_other	7.459
r_dihedral_angle_1_deg	6.857
r_scangle_it	6.13
r_scangle_other	6.127
r_scbond_other	3.745
r_scbond_it	3.736
r_mcangle_it	3.033
r_mcangle_other	3.031
r_mcbond_it	2.112
r_mcbond_other	2.111
r_angle_refined_deg	1.912
r_angle_other_deg	0.651
r_symmetry_nbd_refined	0.338
r_metal_ion_refined	0.248
r_xyhbond_nbd_refined	0.237
r_nbd_refined	0.215
r_nbd_other	0.194
r_symmetry_nbd_other	0.191
r_nbtor_refined	0.179
r_symmetry_xyhbond_nbd_refined	0.135
r_symmetry_xyhbond_nbd_other	0.113
r_chiral_restr	0.101
r_symmetry_nbtor_other	0.082
r_bond_refined_d	0.009
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	1141
Nucleic Acid Atoms
Solvent Atoms	187
Heterogen Atoms	49

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.

9T48 | pdb_00009t48