Experiment: 9ZDI

X-RAY DIFFRACTION

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	298	VAPOR DIFFUSION AGAINST 4.0M Ammonium Sulfate, pH 8.5,

Crystal Properties
Matthews coefficient	Solvent content
1.8	31.85

Symmetry
Space Group	P 1 21 1

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 16M		2024-12-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL12-2	0.77488	SSRL	BL12-2

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.02	25.27	88	0.205	0.089	0.986	6.2	6.1		34060			14.447

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.02	1.078	50.5		3.137	1.427	0.341	1.8	6.1

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	SAD	THROUGHOUT	1.02	25.27	32449	1611	79.05	0.15324	0.15191	0.158	0.18134	0.1849	RANDOM	11.862

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]
-0.72		0.42	0.53		-0.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	23.223
r_dihedral_angle_3_deg	11.869
r_long_range_B_refined	10.35
r_long_range_B_other	9.953
r_scangle_other	7.158
r_dihedral_angle_1_deg	5.612
r_scbond_it	5.424
r_scbond_other	5.419
r_mcangle_other	4.746
r_mcangle_it	4.733

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	23.223
r_dihedral_angle_3_deg	11.869
r_long_range_B_refined	10.35
r_long_range_B_other	9.953
r_scangle_other	7.158
r_dihedral_angle_1_deg	5.612
r_scbond_it	5.424
r_scbond_other	5.419
r_mcangle_other	4.746
r_mcangle_it	4.733
r_rigid_bond_restr	4.243
r_mcbond_it	3.336
r_mcbond_other	3.323
r_angle_refined_deg	1.953
r_angle_other_deg	0.69
r_chiral_restr	0.099
r_bond_refined_d	0.011
r_gen_planes_refined	0.011
r_bond_other_d	0.001
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_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	820
Nucleic Acid Atoms
Solvent Atoms	108
Heterogen Atoms

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.

9ZDI | pdb_00009zdi