9S56 | pdb_00009s56

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2QQI

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293	0.3% Sodium-L ascorbate, 0.3% Choline Chloride, 0.3% D-Panthenol, 0.3% Pyridoxine hydrochloride, 0.3% Thiamine hydrochloride, 0.3% CHAPS, 0.3% CHAPSO, 0.3% Sodium glycocholate hydrate, 0.3% Taurocholic acid sodium salt hydrate, 100 mM Tris/Bicine, 10% PEG 20,000, 20% PEG 500 MME

Crystal Properties
Matthews coefficient	Solvent content
2.42	49.24

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 EIGER2 XE 16M		2024-03-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9762	Diamond	I03

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim 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	1.667	59.521	67.8	0.32	0.324	0.053	0.998	9	37.1		30060

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.667	1.864	12.2		2.442	2.48	0.428	0.76	1.7	33.2

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	1.668	59.521	30060	1480	67.869	0.193	0.1909	0.2007	0.2403	0.2513	21.213

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]
0.125			-0.18		0.055

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	13.512
r_dihedral_angle_6_deg	12.887
r_lrange_it	7.536
r_lrange_other	7.466
r_dihedral_angle_1_deg	7.254
r_dihedral_angle_2_deg	6.605
r_scangle_it	4.583
r_scangle_other	4.581
r_mcangle_other	3.698
r_mcangle_it	3.697

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	13.512
r_dihedral_angle_6_deg	12.887
r_lrange_it	7.536
r_lrange_other	7.466
r_dihedral_angle_1_deg	7.254
r_dihedral_angle_2_deg	6.605
r_scangle_it	4.583
r_scangle_other	4.581
r_mcangle_other	3.698
r_mcangle_it	3.697
r_scbond_it	2.72
r_scbond_other	2.72
r_mcbond_it	2.175
r_mcbond_other	2.173
r_angle_refined_deg	1.486
r_angle_other_deg	0.526
r_xyhbond_nbd_refined	0.221
r_symmetry_xyhbond_nbd_refined	0.201
r_symmetry_nbd_refined	0.194
r_symmetry_nbd_other	0.189
r_nbd_refined	0.188
r_nbtor_refined	0.177
r_nbd_other	0.16
r_symmetry_nbtor_other	0.088
r_chiral_restr	0.072
r_symmetry_xyhbond_nbd_other	0.012
r_bond_refined_d	0.01
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2478
Nucleic Acid Atoms
Solvent Atoms	249
Heterogen Atoms	85

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.