Experiment: 9SQD

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8HHD

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	HEPES 0.1M pH=7.5, 0.2M NaCl 25% PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.41	49.02

Symmetry
Space Group	P 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 X 9M		2025-07-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID30B	0.9677	ESRF	ID30B

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	1.95	72.72	85.9	0.112	0.992	7.4	3.6		45729

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	1.95	2	94.1		0.587	0.819	2.3	3.7

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	1.951	72.715	45725	2392	85.873	0.222	0.22	0.2264	0.2662	0.272	24.637

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]
-0.247	-0.346	1.391	0.765	1.208	-0.514

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.432
r_dihedral_angle_3_deg	12.735
r_dihedral_angle_2_deg	7.224
r_dihedral_angle_1_deg	7.053
r_lrange_it	4.593
r_lrange_other	4.578
r_scangle_it	3.396
r_scangle_other	3.389
r_mcangle_other	2.453
r_mcangle_it	2.452

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.432
r_dihedral_angle_3_deg	12.735
r_dihedral_angle_2_deg	7.224
r_dihedral_angle_1_deg	7.053
r_lrange_it	4.593
r_lrange_other	4.578
r_scangle_it	3.396
r_scangle_other	3.389
r_mcangle_other	2.453
r_mcangle_it	2.452
r_scbond_it	2.127
r_scbond_other	2.119
r_angle_refined_deg	1.669
r_mcbond_it	1.589
r_mcbond_other	1.589
r_angle_other_deg	0.561
r_nbd_refined	0.214
r_symmetry_nbd_other	0.201
r_nbtor_refined	0.174
r_nbd_other	0.172
r_xyhbond_nbd_refined	0.159
r_symmetry_xyhbond_nbd_refined	0.144
r_symmetry_nbd_refined	0.116
r_symmetry_nbtor_other	0.08
r_chiral_restr	0.078
r_metal_ion_refined	0.076
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5106
Nucleic Acid Atoms
Solvent Atoms	204
Heterogen Atoms	165

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.

9SQD | pdb_00009sqd