9SNB | pdb_00009snb

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
2.09	41.26

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		2025-02-25	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	1.75	41.113	90.5	0.109	0.13	0.998	11.9	6.4		22338

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	1.75	1.78	97.3		0.974	1.2	0.553	1.6	5.7

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	NONE	1.75	41.113	22324	1198	90.26	0.164	0.162	0.1726	0.1999	0.2073	19.872

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]
-0.142		0.364	0.269		-0.276

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.107
r_dihedral_angle_4_deg	23.581
r_dihedral_angle_3_deg	14.497
r_dihedral_angle_1_deg	7.484
r_lrange_other	5.461
r_lrange_it	5.458
r_scangle_it	4.223
r_scangle_other	4.222
r_scbond_it	2.717
r_scbond_other	2.716

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.107
r_dihedral_angle_4_deg	23.581
r_dihedral_angle_3_deg	14.497
r_dihedral_angle_1_deg	7.484
r_lrange_other	5.461
r_lrange_it	5.458
r_scangle_it	4.223
r_scangle_other	4.222
r_scbond_it	2.717
r_scbond_other	2.716
r_mcangle_other	2.469
r_mcangle_it	2.468
r_mcbond_it	1.654
r_mcbond_other	1.646
r_angle_refined_deg	1.635
r_angle_other_deg	1.376
r_symmetry_nbd_refined	0.285
r_nbd_refined	0.224
r_symmetry_xyhbond_nbd_refined	0.212
r_symmetry_nbd_other	0.193
r_xyhbond_nbd_refined	0.191
r_nbd_other	0.181
r_nbtor_refined	0.172
r_metal_ion_refined	0.09
r_symmetry_nbtor_other	0.082
r_chiral_restr	0.072
r_bond_refined_d	0.01
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	2056
Nucleic Acid Atoms
Solvent Atoms	157
Heterogen Atoms	38

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.