9XZ8 | pdb_00009xz8

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3QR9

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293.15	200 mM imidazole/malate pH 7.5, 13-17% PEG 4000, 0.5 mM MgCl2, 0.5 mM sodium pyrophosphate, 0.5 mM inhibitor 301f

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.5

Symmetry
Space Group	P 2 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 EIGER2 X 16M		2025-08-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2	0.95373	Australian Synchrotron	MX2

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.6	45.719	100	0.999	13.4	13.7		93026			21.1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.6	1.63	100		0.63	1.4	14

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	THROUGHOUT	1.6	45.719	92943	4817	99.967	0.188	0.1856	0.1956	0.2245	0.2344	RANDOM	23.929

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]
-0.253			0.36		-0.107

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.737
r_dihedral_angle_2_deg	13.167
r_dihedral_angle_3_deg	11.879
r_lrange_other	6.26
r_lrange_it	6.259
r_dihedral_angle_1_deg	6.005
r_scangle_it	4.811
r_scangle_other	4.811
r_scbond_it	3.424
r_scbond_other	3.424

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.737
r_dihedral_angle_2_deg	13.167
r_dihedral_angle_3_deg	11.879
r_lrange_other	6.26
r_lrange_it	6.259
r_dihedral_angle_1_deg	6.005
r_scangle_it	4.811
r_scangle_other	4.811
r_scbond_it	3.424
r_scbond_other	3.424
r_mcangle_other	3.352
r_mcangle_it	3.351
r_mcbond_it	2.376
r_mcbond_other	2.371
r_angle_refined_deg	1.812
r_angle_other_deg	0.625
r_symmetry_nbd_refined	0.274
r_nbd_other	0.254
r_nbd_refined	0.225
r_symmetry_nbd_other	0.198
r_symmetry_xyhbond_nbd_refined	0.198
r_nbtor_refined	0.18
r_chiral_restr	0.158
r_xyhbond_nbd_refined	0.155
r_symmetry_nbtor_other	0.079
r_symmetry_xyhbond_nbd_other	0.057
r_metal_ion_refined	0.018
r_chiral_restr_other	0.011
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4983
Nucleic Acid Atoms
Solvent Atoms	565
Heterogen Atoms	173

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.