Experiment: 9P5A

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
1.96	37.2

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	1.498	22.096	99.709	0.99	18	1		18832

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	1.498	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	1.498	22.096	18832	979	99.709	0.177	0.1752	0.185	0.2067	0.2151	12.266

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]
-0.002			-0.002		0.005

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	19.503
r_dihedral_angle_6_deg	17.289
r_dihedral_angle_3_deg	13.846
r_dihedral_angle_1_deg	6.621
r_lrange_it	4.595
r_lrange_other	4.433
r_scangle_it	3.134
r_scangle_other	3.132
r_scbond_it	2.042
r_scbond_other	2.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	19.503
r_dihedral_angle_6_deg	17.289
r_dihedral_angle_3_deg	13.846
r_dihedral_angle_1_deg	6.621
r_lrange_it	4.595
r_lrange_other	4.433
r_scangle_it	3.134
r_scangle_other	3.132
r_scbond_it	2.042
r_scbond_other	2.04
r_mcangle_it	1.787
r_mcangle_other	1.787
r_angle_refined_deg	1.724
r_mcbond_it	1.186
r_mcbond_other	1.185
r_angle_other_deg	0.597
r_xyhbond_nbd_refined	0.317
r_nbd_refined	0.249
r_symmetry_nbd_other	0.204
r_symmetry_nbd_refined	0.192
r_nbtor_refined	0.184
r_nbd_other	0.167
r_symmetry_xyhbond_nbd_refined	0.167
r_metal_ion_refined	0.099
r_chiral_restr	0.09
r_symmetry_nbtor_other	0.08
r_symmetry_xyhbond_nbd_other	0.04
r_gen_planes_refined	0.011
r_bond_refined_d	0.01
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1001
Nucleic Acid Atoms
Solvent Atoms	129
Heterogen Atoms	20

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.

9P5A | pdb_00009p5a