Experiment: 9SFO

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	9RVW

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293.15	24% PEG 3350, 100 mM MES pH 7.0

Crystal Properties
Matthews coefficient	Solvent content
3.6	65.85

Symmetry
Space Group	P 41 21 2

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 PILATUS3 2M		2021-02-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.87313	ESRF	ID23-2

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	3.42	72.28	99.7	0.376	0.412	0.165	0.914	4.5	5.8		20087

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	3.42	3.69		99.8	0.978	1.068	0.419	0.802		6.1

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3.42	70.396	20005	1027	99.231	0.207	0.204	0.2103	0.2688	0.2668	RANDOM	64.535

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]
2.019			2.019		-4.038

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.945
r_dihedral_angle_6_deg	13.478
r_lrange_it	11.401
r_lrange_other	11.4
r_dihedral_angle_2_deg	8.899
r_scangle_it	7.89
r_scangle_other	7.886
r_dihedral_angle_1_deg	7.593
r_mcangle_it	7.304
r_mcangle_other	7.303

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.945
r_dihedral_angle_6_deg	13.478
r_lrange_it	11.401
r_lrange_other	11.4
r_dihedral_angle_2_deg	8.899
r_scangle_it	7.89
r_scangle_other	7.886
r_dihedral_angle_1_deg	7.593
r_mcangle_it	7.304
r_mcangle_other	7.303
r_scbond_it	4.632
r_scbond_other	4.626
r_mcbond_it	4.385
r_mcbond_other	4.384
r_angle_refined_deg	1.448
r_angle_other_deg	0.489
r_nbd_refined	0.216
r_metal_ion_refined	0.202
r_symmetry_nbd_other	0.201
r_symmetry_nbd_refined	0.188
r_nbd_other	0.186
r_nbtor_refined	0.184
r_xyhbond_nbd_refined	0.176
r_symmetry_xyhbond_nbd_refined	0.171
r_symmetry_nbtor_other	0.081
r_chiral_restr	0.066
r_dihedral_angle_other_2_deg	0.051
r_symmetry_xyhbond_nbd_other	0.039
r_bond_refined_d	0.004
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6588
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	133

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.

9SFO | pdb_00009sfo