Experiment: 9P65

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	4.6	295	1.2 M NaCl and 100 mM AcONa pH 4.6

Crystal Properties
Matthews coefficient	Solvent content
2.09	41.08

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	300	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	1.472	27.489	99	0.99	18	1		20433

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	1.472	1.5			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	1.472	27.489	20433	1003	96.724	0.171	0.1694	0.1694	0.1984	0.1988	19.48

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]
0.001			0.001		-0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.252
r_dihedral_angle_3_deg	11.066
r_dihedral_angle_2_deg	10.032
r_lrange_it	7.605
r_lrange_other	7.603
r_scangle_it	6.444
r_scangle_other	6.44
r_dihedral_angle_1_deg	6.193
r_scbond_it	4.095
r_scbond_other	4.091

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.252
r_dihedral_angle_3_deg	11.066
r_dihedral_angle_2_deg	10.032
r_lrange_it	7.605
r_lrange_other	7.603
r_scangle_it	6.444
r_scangle_other	6.44
r_dihedral_angle_1_deg	6.193
r_scbond_it	4.095
r_scbond_other	4.091
r_mcangle_other	2.872
r_mcangle_it	2.85
r_angle_refined_deg	2.003
r_mcbond_it	1.9
r_mcbond_other	1.898
r_angle_other_deg	0.702
r_xyhbond_nbd_refined	0.46
r_nbd_refined	0.254
r_symmetry_nbd_other	0.197
r_nbtor_refined	0.182
r_nbd_other	0.142
r_chiral_restr	0.118
r_symmetry_nbd_refined	0.101
r_symmetry_nbtor_other	0.081
r_metal_ion_refined	0.044
r_bond_refined_d	0.011
r_gen_planes_refined	0.01
r_symmetry_xyhbond_nbd_refined	0.007
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	74
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.

9P65 | pdb_00009p65