9SNC | pdb_00009snc

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4FIK

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	296	1.5 M sodium citrate, 0.1 M Tris pH 8.0

Crystal Properties
Matthews coefficient	Solvent content
2.13	42.29

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 PILATUS 6M		2025-01-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 11.2C	1.00	ELETTRA	11.2C

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	1.4	35.946	91.8	0.058	0.07	0.999	14.3	5.9		44824

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.4	1.42	94.5		0.656	0.845	0.696	1.8	4.3

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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	NONE	1.4	35.946	44568	2146	91.259	0.136	0.1341	0.1433	0.1759	0.1759	17.636

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]
0.46		-0.172	0.117		-0.43

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.625
r_dihedral_angle_4_deg	22.341
r_dihedral_angle_3_deg	13.311
r_dihedral_angle_1_deg	7.007
r_scangle_it	4.809
r_scangle_other	4.808
r_lrange_it	4.496
r_lrange_other	4.495
r_scbond_it	3.9
r_scbond_other	3.898

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.625
r_dihedral_angle_4_deg	22.341
r_dihedral_angle_3_deg	13.311
r_dihedral_angle_1_deg	7.007
r_scangle_it	4.809
r_scangle_other	4.808
r_lrange_it	4.496
r_lrange_other	4.495
r_scbond_it	3.9
r_scbond_other	3.898
r_rigid_bond_restr	3.856
r_mcangle_other	3.118
r_mcangle_it	3.076
r_mcbond_it	2.59
r_mcbond_other	2.488
r_angle_refined_deg	1.915
r_angle_other_deg	1.51
r_nbd_refined	0.239
r_symmetry_nbd_other	0.199
r_symmetry_nbd_refined	0.199
r_nbd_other	0.188
r_nbtor_refined	0.177
r_xyhbond_nbd_refined	0.135
r_chiral_restr	0.112
r_symmetry_xyhbond_nbd_refined	0.109
r_symmetry_nbtor_other	0.086
r_metal_ion_refined	0.076
r_gen_planes_refined	0.016
r_bond_refined_d	0.015
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2056
Nucleic Acid Atoms
Solvent Atoms	230
Heterogen Atoms	37

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.