9SI2 | pdb_00009si2

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3ZOS

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		277	Protein concentration: 10 mg/ml Ligand concentration: 10 mM Complex formation: The crystals have been grown in presence of the compound CHD-070065. Drop set up: 1:1 (0.1 microL reservoir : 0.1 microL protein solution).

Crystal Properties
Matthews coefficient	Solvent content
2.13	42.41

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		2021-10-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.9999	SLS	X10SA

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	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	2.117	49.19	100	0.268	0.268	6.9	6.8		17583

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.117	2.153	100		1.736	1.736	1.3	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 (Observed)	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	2.12	49.19	16701	871	99.89	0.21524	0.21301	0.2161	0.2573	0.2576	RANDOM	32.982

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]
-2.77			-0.02		2.79

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.492
r_dihedral_angle_4_deg	16.096
r_dihedral_angle_3_deg	14.612
r_dihedral_angle_1_deg	7.1
r_long_range_B_refined	3.526
r_long_range_B_other	3.522
r_angle_refined_deg	1.473
r_angle_other_deg	1.183
r_mcangle_it	0.962
r_mcangle_other	0.962

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.492
r_dihedral_angle_4_deg	16.096
r_dihedral_angle_3_deg	14.612
r_dihedral_angle_1_deg	7.1
r_long_range_B_refined	3.526
r_long_range_B_other	3.522
r_angle_refined_deg	1.473
r_angle_other_deg	1.183
r_mcangle_it	0.962
r_mcangle_other	0.962
r_scangle_other	0.782
r_mcbond_it	0.527
r_mcbond_other	0.527
r_scbond_it	0.446
r_scbond_other	0.446
r_chiral_restr	0.067
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_bond_other_d	0.003
r_gen_planes_other	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2336
Nucleic Acid Atoms
Solvent Atoms	177
Heterogen Atoms	55

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.