9N5W | pdb_00009n5w

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	1 % w/v Polyethylene glycol monomethyl ether 2,000, 0.1 M HEPES pH 7.0, 1 M Succinic acid pH 7.0

Crystal Properties
Matthews coefficient	Solvent content
3.27	62.43

Symmetry
Space Group	P 4 21 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 EIGER2 X 9M		2023-09-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID30B	0.87313	ESRF	ID30B

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	2.06	127.49	100	0.211	0.219	0.057	0.999	13.2	28.2		61736

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)
	2.06	2.11	100		3.136	3.246	0.838	0.714	2	29.3

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	2.06	127.49	61631	3182	99.88	0.199	0.1978	0.2004	0.2193	0.2221	43.212

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]
-0.885			-0.885		1.77

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	19.596
r_dihedral_angle_6_deg	14.459
r_dihedral_angle_3_deg	12.934
r_lrange_it	8.856
r_scangle_it	6.818
r_dihedral_angle_1_deg	6.478
r_mcangle_it	4.971
r_scbond_it	4.706
r_mcbond_it	3.522
r_angle_refined_deg	1.586

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	19.596
r_dihedral_angle_6_deg	14.459
r_dihedral_angle_3_deg	12.934
r_lrange_it	8.856
r_scangle_it	6.818
r_dihedral_angle_1_deg	6.478
r_mcangle_it	4.971
r_scbond_it	4.706
r_mcbond_it	3.522
r_angle_refined_deg	1.586
r_nbtor_refined	0.31
r_nbd_refined	0.198
r_symmetry_nbd_refined	0.175
r_symmetry_xyhbond_nbd_refined	0.144
r_xyhbond_nbd_refined	0.128
r_chiral_restr	0.076
r_ncsr_local_group_1	0.068
r_gen_planes_refined	0.009
r_bond_refined_d	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4700
Nucleic Acid Atoms
Solvent Atoms	200
Heterogen Atoms	29

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.