7Z8U | pdb_00007z8u

Catalytic subunit HisG R56A mutant from Psychrobacter arcticus ATPPRT (HisGZ) in complex with ATP and PRPP

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6FCT

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	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 pH6.0, 0.1M K/Na tartrate

Crystal Properties
Matthews coefficient	Solvent content
1.98	38.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.09	α = 90
b = 33.9	β = 103.52
c = 89.265	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	2019-11-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.54178

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	22.02	93.8	0.108	0.13	0.072	0.989	7.2	3		13035

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	2.05	88.2		0.364	0.453	0.267	0.843		2.6

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	6FCT	2	22.02	12411	623	92.43	0.2239	0.2216	0.23	0.2682	0.27	RANDOM	19.809

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]
-1.84		-0.76	-2.52		4.23

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.525
r_dihedral_angle_3_deg	14.552
r_dihedral_angle_4_deg	13.093
r_dihedral_angle_1_deg	7.929
r_angle_refined_deg	1.623
r_angle_other_deg	1.244
r_chiral_restr	0.067
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.525
r_dihedral_angle_3_deg	14.552
r_dihedral_angle_4_deg	13.093
r_dihedral_angle_1_deg	7.929
r_angle_refined_deg	1.623
r_angle_other_deg	1.244
r_chiral_restr	0.067
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1573
Nucleic Acid Atoms
Solvent Atoms	42
Heterogen Atoms	54

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.