9N8U | pdb_00009n8u

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	25 % v/v Glycerol, 0.05 M Bis-Tris pH 7, 1.4 M Ammonium sulfate

Crystal Properties
Matthews coefficient	Solvent content
2.79	55.99

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 9M		2024-10-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS-II BEAMLINE 17-ID-1	0.920194	NSLS-II	17-ID-1

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	1.74	34.17	100	0.176	0.182	0.048	1	18.9	27		45057

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	1.74	1.77			2.499	2.593	0.69	0.328

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	FREE R-VALUE	1.74	34.17	45056	2314	99.971	0.205	0.2039	0.2038	0.2272	0.227	RANDOM	35.218

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]
-0.278			-0.278		0.556

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.654
r_dihedral_angle_3_deg	12.549
r_lrange_it	10.87
r_dihedral_angle_2_deg	9.132
r_scangle_it	7.689
r_dihedral_angle_1_deg	6.252
r_scbond_it	5.615
r_mcangle_it	4.465
r_mcbond_it	3.208
r_angle_refined_deg	1.825

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.654
r_dihedral_angle_3_deg	12.549
r_lrange_it	10.87
r_dihedral_angle_2_deg	9.132
r_scangle_it	7.689
r_dihedral_angle_1_deg	6.252
r_scbond_it	5.615
r_mcangle_it	4.465
r_mcbond_it	3.208
r_angle_refined_deg	1.825
r_nbtor_refined	0.312
r_symmetry_nbd_refined	0.216
r_nbd_refined	0.199
r_chiral_restr	0.131
r_xyhbond_nbd_refined	0.117
r_symmetry_xyhbond_nbd_refined	0.115
r_bond_refined_d	0.011
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2371
Nucleic Acid Atoms	82
Solvent Atoms	159
Heterogen Atoms	26

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.