6FUA | pdb_00006fua

ATP phosphoribosyltransferase (HisZG ATPPRT) from Psychrobacter arcticus in complex with PRPP and ADP

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5M8H	5M8H partial model

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	277	8mg mL-1 protein (in 20mM Tris pH7, 50mM KCl, 10mM MgCl2, 2mM DTT, 0.5mM histidine) mixed in 1:1 ratio with precipitant solution (11% PEG3350, 100mM bicine pH8.5, 150mM SrCl2, 150mM KBr, 2% 1,6-hexanediol)

Crystal Properties
Matthews coefficient	Solvent content
2.48	50.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 101.57	α = 90
b = 146.24	β = 102.98
c = 93.8	γ = 90

Symmetry
Space Group	C 1 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	CCD	RIGAKU SATURN 944+	Varimax	2017-03-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5418

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	2.8	35.04	99.1	0.192	0.224	0.115	0.986	6.4	3.7		32533

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	2.8	2.95	98.6		1.707	1.998	1.032	0.581	0.8	3.6

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	5M8H partial model	2.8	35.04	30909	1623	98.98	0.2478	0.246	0.25	0.2822	0.29	RANDOM	65.218

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]
3.59		1.19	0.2		-3.92

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.384
r_dihedral_angle_3_deg	16.708
r_dihedral_angle_4_deg	14.067
r_dihedral_angle_1_deg	5.882
r_angle_refined_deg	1.32
r_angle_other_deg	0.934
r_chiral_restr	0.068
r_bond_refined_d	0.008
r_gen_planes_refined	0.005
r_bond_other_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.384
r_dihedral_angle_3_deg	16.708
r_dihedral_angle_4_deg	14.067
r_dihedral_angle_1_deg	5.882
r_angle_refined_deg	1.32
r_angle_other_deg	0.934
r_chiral_restr	0.068
r_bond_refined_d	0.008
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9022
Nucleic Acid Atoms
Solvent Atoms	21
Heterogen Atoms	102

Software

Software
Software Name	Purpose
MOSFLM	data reduction
Aimless	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

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.