9SSO | pdb_00009sso

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6Y2E

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	0.1 M Sodium HEPES; MOPS (acid), 30% w/v (40% v/v PEG 500* MME; 20 % w/v PEG 20000), 0.1M Ethylene glycol

Crystal Properties
Matthews coefficient	Solvent content
2.62	53.04

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 EIGER X 16M		2024-05-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, DESY BEAMLINE P11	1.0332	PETRA III, DESY	P11

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.6	49.38	99.94	0.999	16.5	26.5		93746

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.6	1.657	99.92		0.567

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	1.6	49.38	93742	4654	99.946	0.196	0.1942	0.2065	0.2242	0.2341	28.312

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]
-1.728			2.569		-0.84

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.134
r_dihedral_angle_6_deg	16.015
r_dihedral_angle_2_deg	9.038
r_dihedral_angle_1_deg	7.121
r_lrange_it	6.979
r_lrange_other	6.979
r_dihedral_angle_other_2_deg	6.414
r_scangle_it	5.932
r_scangle_other	5.932
r_scbond_other	3.957

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.134
r_dihedral_angle_6_deg	16.015
r_dihedral_angle_2_deg	9.038
r_dihedral_angle_1_deg	7.121
r_lrange_it	6.979
r_lrange_other	6.979
r_dihedral_angle_other_2_deg	6.414
r_scangle_it	5.932
r_scangle_other	5.932
r_scbond_other	3.957
r_scbond_it	3.956
r_mcangle_it	3.654
r_mcangle_other	3.654
r_mcbond_it	2.631
r_mcbond_other	2.615
r_dihedral_angle_other_3_deg	1.657
r_angle_refined_deg	1.58
r_angle_other_deg	0.542
r_symmetry_nbd_refined	0.213
r_nbd_refined	0.21
r_nbd_other	0.196
r_symmetry_nbd_other	0.195
r_nbtor_refined	0.183
r_symmetry_xyhbond_nbd_refined	0.139
r_xyhbond_nbd_refined	0.13
r_symmetry_nbtor_other	0.084
r_chiral_restr	0.082
r_bond_refined_d	0.009
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4707
Nucleic Acid Atoms
Solvent Atoms	269
Heterogen Atoms	78

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.