9Z0Z | pdb_00009z0z

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	9DYS

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH	7.4	291	Imidazole 0.1 M pH 6.9, Polyethylene glycol 6,000 20.0% w/v

Crystal Properties
Matthews coefficient	Solvent content
2.17	43.4

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	298	PIXEL	DECTRIS EIGER R 4M		2024-10-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.541838

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	3.1	27.39	99.8	0.265	0.28	0.089	0.983	9.9	9.5		10389

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	3.1	3.31		100	0.587	0.619	0.195	0.903		9.8

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	3.1	27.39	9831	528	99.69	0.14676	0.14283	0.1498	0.21843	0.2114	RANDOM	8.1

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]
0.1			0.15		-0.25

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.403
r_dihedral_angle_2_deg	8.337
r_dihedral_angle_1_deg	7.582
r_long_range_B_refined	6.054
r_long_range_B_other	6.054
r_scangle_other	3.473
r_mcangle_it	2.262
r_mcangle_other	2.261
r_scbond_it	2.159
r_scbond_other	2.159

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.403
r_dihedral_angle_2_deg	8.337
r_dihedral_angle_1_deg	7.582
r_long_range_B_refined	6.054
r_long_range_B_other	6.054
r_scangle_other	3.473
r_mcangle_it	2.262
r_mcangle_other	2.261
r_scbond_it	2.159
r_scbond_other	2.159
r_angle_refined_deg	1.819
r_mcbond_it	1.436
r_mcbond_other	1.436
r_angle_other_deg	0.604
r_chiral_restr	0.075
r_bond_refined_d	0.014
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_dihedral_angle_4_deg
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4352
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	34

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.