7DSR | pdb_00007dsr

Anthranilate phosphoribosyltransferase variant Gly141Asn from Saccharomyces cerevisiae in complex with 4-fluoroanthranilate

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7DSM

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		287	20 % PEG 4000, 0.1 M Tris PH 8.0

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.35

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.209	α = 90
b = 87.238	β = 90
c = 109.325	γ = 90

Symmetry
Space Group	P 21 21 21

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 PILATUS3 6M		2020-06-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL18U1	0.97915	SSRF	BL18U1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim I (All)	Rpim I (All)	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	2.5	50	99.8	0.099	0.027	31.8	12.9		26794

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.5	2.54	100		0.507	0.145	4.2	11.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	7DSM	2.5	46.36	25444	1277	99.45	0.2059	0.2027	0.21	0.267	0.27	RANDOM	46.108

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]
-2.26			6.75		-4.48

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.117
r_dihedral_angle_3_deg	19.212
r_dihedral_angle_4_deg	16.716
r_dihedral_angle_1_deg	6.337
r_angle_refined_deg	1.38
r_angle_other_deg	1.291
r_chiral_restr	0.065
r_bond_refined_d	0.006
r_gen_planes_refined	0.005
r_bond_other_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.117
r_dihedral_angle_3_deg	19.212
r_dihedral_angle_4_deg	16.716
r_dihedral_angle_1_deg	6.337
r_angle_refined_deg	1.38
r_angle_other_deg	1.291
r_chiral_restr	0.065
r_bond_refined_d	0.006
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5387
Nucleic Acid Atoms
Solvent Atoms	70
Heterogen Atoms	11

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

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.