Experiment: 9N8L

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2R6S

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		295	0.15 M Potassium chloride, 25 % v/v Glycerol, 0.05 M Bis-Tris pH 7, 1.6 M Ammonium sulfate

Crystal Properties
Matthews coefficient	Solvent content
2.78	55.82

Symmetry
Space Group	I 4 2 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 EIGER X 16M		2024-10-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS-II BEAMLINE 17-ID-2	0.979361	NSLS-II	17-ID-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	1.42	34.41	100	0.106	0.114	0.041	0.999	15.9	14.8		81604

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	1.42	1.44	100		1.642	1.798	0.726	0.359		12

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	1.42	34.41	77643	3959	99.99	0.15137	0.15049	0.1488	0.16812	0.1691	RANDOM	23.814

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]
-1.62			-1.62		3.23

RMS Deviations
Key	Refinement Restraint Deviation
r_rigid_bond_restr	33.506
r_long_range_B_refined	26.972
r_long_range_B_other	23.277
r_dihedral_angle_2_deg	13.608
r_scangle_other	12.926
r_dihedral_angle_3_deg	12.555
r_scbond_it	8.771
r_scbond_other	8.77
r_mcangle_other	8.172
r_mcangle_it	8.119

RMS Deviations
Key	Refinement Restraint Deviation
r_rigid_bond_restr	33.506
r_long_range_B_refined	26.972
r_long_range_B_other	23.277
r_dihedral_angle_2_deg	13.608
r_scangle_other	12.926
r_dihedral_angle_3_deg	12.555
r_scbond_it	8.771
r_scbond_other	8.77
r_mcangle_other	8.172
r_mcangle_it	8.119
r_dihedral_angle_1_deg	6.424
r_mcbond_other	5.651
r_mcbond_it	5.556
r_angle_refined_deg	1.434
r_angle_other_deg	0.527
r_chiral_restr	0.078
r_gen_planes_other	0.008
r_gen_planes_refined	0.006
r_bond_refined_d	0.005
r_bond_other_d
r_dihedral_angle_4_deg
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_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2332
Nucleic Acid Atoms	82
Solvent Atoms	298
Heterogen Atoms	20

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.

9N8L | pdb_00009n8l