7AZA | pdb_00007aza

Perdeuterated E65Q-TIM complexed with PHOSPHOGLYCOLOHYDROXAMATE

X-RAY DIFFRACTION - NEUTRON DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2VXN

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		293.15	0.1 M sodium acetate, 1 mM Na EDTA, 1 mM DTT,18% PEG6000

Crystal Properties
Matthews coefficient	Solvent content
2.47	50.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 98.323	α = 90
b = 52.678	β = 117.86
c = 58.665	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	293	PIXEL	DECTRIS PILATUS3 6M		2016-11-01	M	SINGLE WAVELENGTH
2	1	neutron	293	IMAGE PLATE	CUSTOM-MADE		2018-03-28	L	LAUE

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)	0.89	PETRA III, EMBL c/o DESY	P14 (MX2)
2	NUCLEAR REACTOR	ILL BEAMLINE LADI III	2.7-3.5	ILL	LADI III

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	R Split (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	1.1	45.01	96			0.043		0.999		14.77	3.2		104600
2	1.8	40	78			0.194		0.955		3.8	5.2		19145

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	R Split (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.1	1.16				0.962		0.663		2.1
2	1.8	1.9				0.514		0.666		2.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	1.1	45.01		1.35		104575	5194	96.17		0.1445	0.1438	0.14	0.1577	0.16		22.83
NEUTRON DIFFRACTION	MOLECULAR REPLACEMENT	1.8	30.5502				19144	965	77.37		0.2221	0.2202		0.2596

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]

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1871
Nucleic Acid Atoms
Solvent Atoms	381
Heterogen Atoms	14

Software

Software
Software Name	Purpose
CNS	refinement
PHENIX	refinement
XDS	data reduction
LAUEGEN	data reduction
XSCALE	data scaling
SCALA	data scaling
PHASER	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.