Experiment: 9T49

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: 20.4 PCP-IP8: 5mM Precipitant condition: 27% PEG 6K, 0.1M NaOAc pH 5, 0.2M LiCl, 10mM MgCl2 Ratio: 1:1

Crystal Properties
Matthews coefficient	Solvent content
2.9	57.8

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		2023-06-09	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	49.57	96.7	0.04	0.99	15.3	20.8		29778			15

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			0.4	0.8	2.2

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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.5	49.57	29778	1560	96.704	0.154	0.1531	0.1536	0.1792	0.1787	17.614

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]
0.253	0.127		0.253		-0.822

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.85
r_dihedral_angle_3_deg	12.059
r_lrange_it	9.044
r_lrange_other	8.808
r_dihedral_angle_1_deg	6.659
r_scangle_it	6.631
r_scangle_other	6.628
r_dihedral_angle_2_deg	6.283
r_scbond_other	4.172
r_scbond_it	4.169

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.85
r_dihedral_angle_3_deg	12.059
r_lrange_it	9.044
r_lrange_other	8.808
r_dihedral_angle_1_deg	6.659
r_scangle_it	6.631
r_scangle_other	6.628
r_dihedral_angle_2_deg	6.283
r_scbond_other	4.172
r_scbond_it	4.169
r_mcangle_it	3.27
r_mcangle_other	3.267
r_mcbond_other	2.152
r_mcbond_it	2.15
r_angle_refined_deg	2.144
r_angle_other_deg	0.707
r_symmetry_nbd_refined	0.269
r_symmetry_xyhbond_nbd_refined	0.253
r_nbd_other	0.246
r_xyhbond_nbd_refined	0.224
r_nbd_refined	0.218
r_symmetry_nbd_other	0.184
r_nbtor_refined	0.181
r_metal_ion_refined	0.142
r_chiral_restr	0.109
r_symmetry_nbtor_other	0.082
r_bond_refined_d	0.014
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1171
Nucleic Acid Atoms
Solvent Atoms	205
Heterogen Atoms	50

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.

9T49 | pdb_00009t49