Experiment: 9P0Z

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3A8Z

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		295	1.2 M sodium chloride, 100 mM sodium acetate, pH 4.6

Crystal Properties
Matthews coefficient	Solvent content
2	38.35

Symmetry
Space Group	P 43 21 2

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	Bruker PHOTON II		2024-07-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER TURBO X-RAY SOURCE	1.54184

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	1.499	27.001	99	0.9	16	20		19135

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	1.5	10			0.99

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	1.499	27.001	19135	941	99.755	0.207	0.206	0.2132	0.2361	0.243	8.78

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]
-0.011			-0.011		0.022

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.316
r_dihedral_angle_3_deg	11.874
r_dihedral_angle_2_deg	7.169
r_dihedral_angle_1_deg	6.553
r_lrange_it	3.726
r_lrange_other	3.641
r_scangle_it	2.838
r_scangle_other	2.836
r_angle_refined_deg	1.854
r_scbond_it	1.814

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.316
r_dihedral_angle_3_deg	11.874
r_dihedral_angle_2_deg	7.169
r_dihedral_angle_1_deg	6.553
r_lrange_it	3.726
r_lrange_other	3.641
r_scangle_it	2.838
r_scangle_other	2.836
r_angle_refined_deg	1.854
r_scbond_it	1.814
r_scbond_other	1.813
r_mcangle_other	1.377
r_mcangle_it	1.375
r_mcbond_it	0.894
r_mcbond_other	0.889
r_angle_other_deg	0.654
r_xyhbond_nbd_refined	0.388
r_symmetry_xyhbond_nbd_refined	0.329
r_nbd_refined	0.265
r_symmetry_nbd_other	0.202
r_nbtor_refined	0.184
r_nbd_other	0.13
r_chiral_restr	0.097
r_symmetry_nbtor_other	0.078
r_metal_ion_refined	0.071
r_symmetry_nbd_refined	0.05
r_bond_refined_d	0.009
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1001
Nucleic Acid Atoms
Solvent Atoms	86
Heterogen Atoms	8

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.

9P0Z | pdb_00009p0z