4JL5 | pdb_00004jl5

A high resolution structure of Aquifex Adenylate kinase with 2 ADP's

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.4	295	0.1M Sodium Acetate trihydrate, 0.2M Ammonium Acetate, 30% w/v Polyethylene Glycol 4000, 20mM MgCl2, 20mM ADP , pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.14	42.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.17	α = 90
b = 69.56	β = 90
c = 85.39	γ = 90

Symmetry
Space Group	P 21 21 21

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	MARMOSAIC 300 mm CCD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-B	0.99186	APS	23-ID-B

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.24	28.96	99.4	22.1		1560689	111370	2	2

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	1.24	1.31	96.2		0.427	5.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	1.24	28.96	1.34	111278	5580	99.35	0.1317	0.1303	0.133	0.1585	0.1597

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]
0.2067			-0.2033		-0.0034

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	17.265
f_angle_d	1.501
f_chiral_restr	0.077
f_bond_d	0.01
f_plane_restr	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3236
Nucleic Acid Atoms
Solvent Atoms	797
Heterogen Atoms	108

Software

Software
Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing