Experiment: 9SN9

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5707

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		277	Precipitating solution : - 25% PEG 4000 - 10% MPD 10% - 100 mM MES pH 6.5 Protein solution : - 10 mg/mL protein in Tris-HCl 30 mM pH 8.0

Crystal Properties
Matthews coefficient	Solvent content
2.16	43.17

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		2025-01-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM07	0.979506	ESRF	BM07

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	1.8	47.72	99.2	0.077	1	8.9	4.1		39704

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	1.8	1.84	98.7		0.567	0.63	1.7

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	1.802	47.715	39659	1960	98.888	0.173	0.1709	0.1709	0.2145	0.2146	21.832

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]
-0.521			-1.528		2.048

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.862
r_dihedral_angle_3_deg	14.8
r_dihedral_angle_2_deg	10.535
r_lrange_it	7.739
r_lrange_other	7.719
r_dihedral_angle_1_deg	6.38
r_scangle_it	6.312
r_scangle_other	6.311
r_scbond_it	4.316
r_scbond_other	4.315

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.862
r_dihedral_angle_3_deg	14.8
r_dihedral_angle_2_deg	10.535
r_lrange_it	7.739
r_lrange_other	7.719
r_dihedral_angle_1_deg	6.38
r_scangle_it	6.312
r_scangle_other	6.311
r_scbond_it	4.316
r_scbond_other	4.315
r_mcangle_it	3.35
r_mcangle_other	3.349
r_mcbond_it	2.613
r_mcbond_other	2.608
r_angle_refined_deg	1.964
r_angle_other_deg	0.66
r_nbd_other	0.235
r_symmetry_nbd_refined	0.232
r_nbd_refined	0.227
r_symmetry_nbd_other	0.191
r_nbtor_refined	0.184
r_xyhbond_nbd_refined	0.151
r_symmetry_xyhbond_nbd_refined	0.149
r_ncsr_local_group_1	0.111
r_chiral_restr	0.108
r_metal_ion_refined	0.09
r_symmetry_nbtor_other	0.083
r_bond_refined_d	0.015
r_gen_planes_refined	0.012
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3417
Nucleic Acid Atoms
Solvent Atoms	215
Heterogen Atoms	57

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.

9SN9 | pdb_00009sn9