9ZXN | pdb_00009zxn

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5FQD

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.2M ammonium acetate, 0.1M Bis Tris pH 5.5-6.5, and 25% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.46	49.96

Symmetry
Space Group	P 21 21 21

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		2024-10-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS-II BEAMLINE 17-ID-1	.92019	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	2.07	44.93	97.51	0.1548	0.1649	0.05607	0.997	9.41	8.5		59921			26.22

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	2.07	2.09			0.9613	1.026	0.3538	0.562	1.29

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	2.07	44.93	58271	2852	99.916	0.19	0.1877	0.1887	0.2353	0.2356	37.201

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]
-0.804			1.738		-0.933

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.41
r_dihedral_angle_6_deg	14.051
r_dihedral_angle_2_deg	11.189
r_lrange_it	8.466
r_lrange_other	8.447
r_dihedral_angle_1_deg	7.945
r_scangle_it	6.022
r_scangle_other	6.021
r_mcangle_it	4.926
r_mcangle_other	4.925

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.41
r_dihedral_angle_6_deg	14.051
r_dihedral_angle_2_deg	11.189
r_lrange_it	8.466
r_lrange_other	8.447
r_dihedral_angle_1_deg	7.945
r_scangle_it	6.022
r_scangle_other	6.021
r_mcangle_it	4.926
r_mcangle_other	4.925
r_scbond_it	3.827
r_scbond_other	3.826
r_mcbond_it	3.142
r_mcbond_other	3.142
r_angle_refined_deg	1.626
r_angle_other_deg	0.542
r_nbd_other	0.26
r_symmetry_nbd_refined	0.231
r_symmetry_nbd_other	0.212
r_nbd_refined	0.204
r_xyhbond_nbd_refined	0.189
r_nbtor_refined	0.176
r_symmetry_xyhbond_nbd_refined	0.141
r_symmetry_nbtor_other	0.09
r_chiral_restr	0.077
r_symmetry_xyhbond_nbd_other	0.031
r_bond_refined_d	0.006
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6253
Nucleic Acid Atoms
Solvent Atoms	232
Heterogen Atoms	61

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.

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