9N8K | pdb_00009n8k

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	10 % v/v Glycerol, 0.05 M MES pH 5.5, 1.5 M Ammonium sulfate

Crystal Properties
Matthews coefficient	Solvent content
2.78	55.75

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 4M		2024-09-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-3	0.967697	ESRF	MASSIF-3

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	1.77	42.66	99.4	0.17	0.176	0.046	0.998	13.5	27.7		42265

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	1.77	1.81	99.4		1.588	1.643	0.421	0.864	2.6	28.8

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	1.77	42.66	40151	2107	99.26	0.17476	0.17309	0.1865	0.20508	0.2111	RANDOM	29.993

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]
4.04			4.04		-8.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	25.077
r_long_range_B_refined	21.012
r_dihedral_angle_3_deg	12.687
r_rigid_bond_restr	12.268
r_scbond_it	10.709
r_mcangle_it	9.897
r_mcbond_it	6.876
r_dihedral_angle_1_deg	6.63
r_angle_refined_deg	1.84
r_chiral_restr	0.124

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	25.077
r_long_range_B_refined	21.012
r_dihedral_angle_3_deg	12.687
r_rigid_bond_restr	12.268
r_scbond_it	10.709
r_mcangle_it	9.897
r_mcbond_it	6.876
r_dihedral_angle_1_deg	6.63
r_angle_refined_deg	1.84
r_chiral_restr	0.124
r_bond_refined_d	0.012
r_gen_planes_refined	0.01
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_4_deg
r_gen_planes_other
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_other
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2342
Nucleic Acid Atoms	82
Solvent Atoms	234
Heterogen Atoms	46

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.