9F94 | pdb_00009f94

Complex of phenazine biosynthesis enzyme PhzF with 2-amino-5-(3-hydroxyphenyl)benzoic acid

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1U1W	chain A

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	2-amino-5-(3-hydroxyphenyl)benzoic acid (50 mM), sodium formate (20 mM), ammonium acetate (20 mM), trisodium citrate (20 mM), sodium potassium L-tartrate (20 mM), sodium oxamate (20 mM), PEG 1000 (12.5%), PEG 3350 (12.5%), (R,S)-2-methyl-2,4-pentanediol (12.5%), MES/imidazole (pH 6.5, 72 mM)

Crystal Properties
Matthews coefficient	Solvent content
2.13	42.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.269	α = 90
b = 56.269	β = 90
c = 156.465	γ = 120

Symmetry
Space Group	P 32 2 1

Diffraction

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		2021-11-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, DESY BEAMLINE P11	1.0332	PETRA III, DESY	P11

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	1.32	48.73	99.9	0.042	0.043	0.01	1	29.1	19		68691

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.32	1.39			0.716	0.739	0.18	0.909	2.9	16.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.32	48.73	1.36	68616	3519	99.81	0.1256	0.1245	0.1377	0.1453	0.1515

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	12.321
f_angle_d	0.989
f_chiral_restr	0.082
f_plane_restr	0.011
f_bond_d	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2113
Nucleic Acid Atoms
Solvent Atoms	270
Heterogen Atoms	24

Software

Software
Software Name	Purpose
autoPROC	data processing
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PHENIX	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.