Experiment: 9ZDH

X-RAY DIFFRACTION

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	298	VAPOR DIFFUSION AGAINST 3.2M NA,K PHOSPHATE, pH 7.0

Crystal Properties
Matthews coefficient	Solvent content
1.9	35.38

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 16M		2023-11-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL12-2	0.97946	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	1.357	33.276	89.7	0.447	0.138	0.979	6.4	10.2		17219			20.31

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	1.357	1.5	57.5		3.708	1.216	0.837	1.5	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-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	SAD	FREE R-VALUE	1.36	33.28	17219	869	57.8	0.172	0.1718	0.213	0.2132	14.35

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]
-0.033			0.343		-0.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	11.169
r_dihedral_angle_1_deg	5.736
r_dihedral_angle_2_deg	5.215
r_scangle_it	4.985
r_scangle_other	4.983
r_scbond_it	3.265
r_scbond_other	3.264
r_mcangle_other	2.216
r_mcangle_it	2.205
r_angle_refined_deg	1.589

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	11.169
r_dihedral_angle_1_deg	5.736
r_dihedral_angle_2_deg	5.215
r_scangle_it	4.985
r_scangle_other	4.983
r_scbond_it	3.265
r_scbond_other	3.264
r_mcangle_other	2.216
r_mcangle_it	2.205
r_angle_refined_deg	1.589
r_mcbond_it	1.398
r_mcbond_other	1.372
r_angle_other_deg	0.565
r_nbd_refined	0.239
r_nbtor_refined	0.186
r_xyhbond_nbd_refined	0.169
r_nbd_other	0.156
r_chiral_restr	0.085
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_dihedral_angle_4_deg
r_nbtor_other
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_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1233
Nucleic Acid Atoms
Solvent Atoms	203
Heterogen Atoms	4

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.

9ZDH | pdb_00009zdh