Experiment: 9QS9

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	293	23.8% PEG3350, 0.2M magnesium chloride, 0.1M bis-Tris pH 5.5

Crystal Properties
Matthews coefficient	Solvent content
2.5	50.8

Symmetry
Space Group	P 1 21 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 EIGER2 S 16M		2024-07-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9537	Diamond	I04

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.44	102.9	100	0.068	0.998	11.2	6.9		169690

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.44	1.47			2.101	0.299

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	1.441	70.425	166107	1951	97.868	0.222	0.222	0.2296	0.2395	0.2457	28.045

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]
-0.655		0.469	-0.734		1.031

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	13.849
r_dihedral_angle_3_deg	9.58
r_dihedral_angle_1_deg	5.877
r_dihedral_angle_2_deg	4.915
r_lrange_it	4.299
r_lrange_other	4.275
r_mcangle_it	2.086
r_mcangle_other	2.086
r_scangle_it	2.069
r_scangle_other	2.069

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	13.849
r_dihedral_angle_3_deg	9.58
r_dihedral_angle_1_deg	5.877
r_dihedral_angle_2_deg	4.915
r_lrange_it	4.299
r_lrange_other	4.275
r_mcangle_it	2.086
r_mcangle_other	2.086
r_scangle_it	2.069
r_scangle_other	2.069
r_scbond_it	1.207
r_scbond_other	1.207
r_mcbond_it	1.193
r_mcbond_other	1.193
r_angle_refined_deg	0.987
r_angle_other_deg	0.425
r_dihedral_angle_other_2_deg	0.336
r_nbd_other	0.219
r_nbd_refined	0.206
r_symmetry_nbd_other	0.195
r_nbtor_refined	0.167
r_symmetry_xyhbond_nbd_refined	0.122
r_xyhbond_nbd_refined	0.101
r_symmetry_nbd_refined	0.093
r_symmetry_nbtor_other	0.081
r_ncsr_local_group_6	0.076
r_ncsr_local_group_4	0.075
r_ncsr_local_group_12	0.075
r_ncsr_local_group_14	0.074
r_ncsr_local_group_3	0.073
r_ncsr_local_group_9	0.073
r_ncsr_local_group_15	0.071
r_ncsr_local_group_5	0.07
r_ncsr_local_group_7	0.069
r_ncsr_local_group_10	0.067
r_ncsr_local_group_1	0.066
r_ncsr_local_group_11	0.066
r_ncsr_local_group_13	0.062
r_ncsr_local_group_2	0.059
r_ncsr_local_group_8	0.051
r_chiral_restr	0.046
r_bond_refined_d	0.003
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5626
Nucleic Acid Atoms	396
Solvent Atoms	693
Heterogen Atoms	7

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.

9QS9 | pdb_00009qs9