Experiment: 9N57

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	0.08 M Sodium chloride, 0.04 M Sodium cacodylate trihydrate pH 7.0, 30 % v/v (+/-)-2-Methyl-2,4-pentanediol, 0.012 M Spermine tetrahydrochloride

Crystal Properties
Matthews coefficient	Solvent content
3.37	63.52

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		2024-04-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS-II BEAMLINE 17-ID-2	0.979338	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	1.64	33.43	100	0.181	0.193	0.066	0.996	10	16.3		62305

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)
	1.64	1.67	100		4.584	4.902	1.729	0.26	0.8	15.6

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	1.64	33.427	62304	3057	99.974	0.167	0.1646	0.1658	0.203	0.2052	34.226

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]
3.033			3.033		-6.066

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	30.14
r_scangle_it	28.252
r_scbond_it	21.928
r_mcangle_it	17.455
r_mcbond_it	13.937
r_dihedral_angle_2_deg	13.914
r_dihedral_angle_6_deg	13.884
r_dihedral_angle_3_deg	12.628
r_dihedral_angle_1_deg	5.852
r_rigid_bond_restr	3.885

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	30.14
r_scangle_it	28.252
r_scbond_it	21.928
r_mcangle_it	17.455
r_mcbond_it	13.937
r_dihedral_angle_2_deg	13.914
r_dihedral_angle_6_deg	13.884
r_dihedral_angle_3_deg	12.628
r_dihedral_angle_1_deg	5.852
r_rigid_bond_restr	3.885
r_angle_refined_deg	1.436
r_nbtor_refined	0.306
r_nbd_refined	0.203
r_symmetry_nbd_refined	0.163
r_xyhbond_nbd_refined	0.16
r_symmetry_xyhbond_nbd_refined	0.105
r_chiral_restr	0.071
r_bond_refined_d	0.012
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2298
Nucleic Acid Atoms
Solvent Atoms	168
Heterogen Atoms	8

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.

9N57 | pdb_00009n57