9SP9 | pdb_00009sp9

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		278	Protein concentration: 9.00 mg/ml Ligand concentration: 2 mM Complex formation: The crystals have been grown in presence of the compound CHD-062411-2. Drop set up: 1:1 (0.1 microL reservoir : 0.1 microL protein solution).

Crystal Properties
Matthews coefficient	Solvent content
2.23	44.79

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 PILATUS 6M		2020-01-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	0.9796	CLSI	08ID-1

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	2.588	53.67	82.4	0.282	0.282	6.9	7.9		8332

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	2.588	2.757	24.4		1.766	1.766	1.2	8

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	2.59	53.67	7902	430	82.32	0.19594	0.19235	0.1978	0.26457	0.2622	RANDOM	44.716

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]
-1.65			-0.3		1.95

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.821
r_dihedral_angle_4_deg	15.395
r_dihedral_angle_3_deg	14.832
r_long_range_B_refined	7.181
r_long_range_B_other	7.172
r_dihedral_angle_1_deg	5.973
r_scangle_other	5.127
r_mcangle_other	4.943
r_mcangle_it	4.942
r_scbond_it	3.101

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.821
r_dihedral_angle_4_deg	15.395
r_dihedral_angle_3_deg	14.832
r_long_range_B_refined	7.181
r_long_range_B_other	7.172
r_dihedral_angle_1_deg	5.973
r_scangle_other	5.127
r_mcangle_other	4.943
r_mcangle_it	4.942
r_scbond_it	3.101
r_scbond_other	3.101
r_mcbond_it	2.989
r_mcbond_other	2.985
r_angle_refined_deg	1.212
r_angle_other_deg	0.936
r_chiral_restr	0.066
r_bond_refined_d	0.008
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001
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	2217
Nucleic Acid Atoms
Solvent Atoms	85
Heterogen Atoms	43

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.