Experiment: 9P58

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 sodium chloride, 100 mM sodium acetate, pH 4.6

Crystal Properties
Matthews coefficient	Solvent content
1.98	38.02

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	1.492	27.659	99	0.99	18	1		19131

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	1.492	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	1.492	27.659	19131	944	98.965	0.228	0.2255	0.2345	0.2685	0.2668	10.808

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]
0.003			0.003		-0.005

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.976
r_dihedral_angle_3_deg	11.427
r_dihedral_angle_2_deg	7.627
r_dihedral_angle_1_deg	6.647
r_lrange_it	4.475
r_lrange_other	4.266
r_scangle_it	3.036
r_scangle_other	3.034
r_scbond_it	1.858
r_scbond_other	1.857

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.976
r_dihedral_angle_3_deg	11.427
r_dihedral_angle_2_deg	7.627
r_dihedral_angle_1_deg	6.647
r_lrange_it	4.475
r_lrange_other	4.266
r_scangle_it	3.036
r_scangle_other	3.034
r_scbond_it	1.858
r_scbond_other	1.857
r_angle_refined_deg	1.736
r_mcangle_other	1.675
r_mcangle_it	1.671
r_mcbond_it	1.09
r_mcbond_other	1.089
r_angle_other_deg	0.597
r_xyhbond_nbd_refined	0.373
r_nbd_refined	0.254
r_symmetry_xyhbond_nbd_refined	0.238
r_symmetry_nbd_other	0.198
r_nbtor_refined	0.181
r_nbd_other	0.174
r_metal_ion_refined	0.093
r_chiral_restr	0.09
r_symmetry_nbtor_other	0.079
r_symmetry_nbd_refined	0.063
r_gen_planes_refined	0.009
r_bond_refined_d	0.008
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	90
Heterogen Atoms	8

Software
Software Name	Purpose
REFMAC	refinement

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.

9P58 | pdb_00009p58