6FD9 | pdb_00006fd9

Catalytic subunit HisG from Psychrobacter arcticus ATP phosphoribosyltransferase (HisZG ATPPRT) in complex with AMP

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6.5	277	10mg/ml protein in 20mM Tris HCl pH8.0, 50mM KCl, 10mM MgCl2, 2mM DTT mixed 1:1 with 32% PEG 3350, 0.1M MOPS pH6.5, 0.1M K/Na tartrate

Crystal Properties
Matthews coefficient	Solvent content
2.12	42.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.82	α = 90
b = 33.94	β = 105.36
c = 92.407	γ = 90

Symmetry
Space Group	I 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+	mirrors	2017-06-06	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	2.2	26.61	93	0.168	0.199	0.105	0.981	5.8	3.6		10299

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	2.2	2.27	87.9		0.549	0.645	0.336	0.706		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 chain E	2.2	26.61	9789	510	93.23	0.1874	0.185	0.19	0.2327	0.24	RANDOM	25.922

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]
-1.62		0.09	-0.93		2.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.367
r_dihedral_angle_4_deg	13.429
r_dihedral_angle_3_deg	13.078
r_dihedral_angle_1_deg	6.781
r_angle_refined_deg	1.308
r_angle_other_deg	0.9
r_chiral_restr	0.071
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	38.367
r_dihedral_angle_4_deg	13.429
r_dihedral_angle_3_deg	13.078
r_dihedral_angle_1_deg	6.781
r_angle_refined_deg	1.308
r_angle_other_deg	0.9
r_chiral_restr	0.071
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	1607
Nucleic Acid Atoms
Solvent Atoms	86
Heterogen Atoms	23

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.