Experiment: 4X8O

Crystal structure of E. coli Adenylate kinase Y171W mutant in complex with inhibitor Ap5a

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1AKE

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	291	28% PEG 4K, 0.1 M NaCit., 0.2 M AmAc

Crystal Properties
Matthews coefficient	Solvent content
2.51	51.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.257	α = 90
b = 72.654	β = 90
c = 79.48	γ = 90

Symmetry
Space Group	P 21 21 2

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	Bruker Platinum 135		2014-01-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER AXS MICROSTAR-H	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.1	41.2	99.7	0.09	32	14.8		28449

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.18	98.1		0.363	6.48	4.88

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-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1ake	2.1	41.129	28378	1437	99.58	0.1803	0.1771	0.2395	0.2071

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	13.605
f_angle_d	0.856
f_chiral_restr	0.029
f_plane_restr	0.005
f_bond_d	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3316
Nucleic Acid Atoms
Solvent Atoms	337
Heterogen Atoms	117

Software

Software
Software Name	Purpose
PHENIX	refinement
SAINT	data reduction
SADABS	data scaling
PHASER	phasing