3GMT

Crystal structure of adenylate kinase from burkholderia pseudomallei

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	290	HAMPTON SCREEN, B5: 30% PEG 4000, 200MM LI2SO4, 100MM TRIS PH 8,, VAPOR DIFFUSION, SITTING DROP, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
2.27	46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.23	α = 90
b = 66	β = 113.69
c = 63.76	γ = 90

Symmetry
Space Group	P 1 21 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	ADSC QUANTUM Q315r		2009-01-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X8C	0.9791	NSLS	X8C

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	20	99.5	0.072	17.02	7.4	27839	27703		-3	42.51

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.15	99.8		0.618	0.618	3.1	7.6	2051

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	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	SAD	THROUGHOUT	2.1	20	27715	26320	1395	99.8	0.238	0.238	0.235	0.2362	0.295	0.2948	RANDOM	29.82

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]
-0.53		-0.19	1.7		-1.32

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.292
r_dihedral_angle_4_deg	19.387
r_dihedral_angle_3_deg	14.881
r_dihedral_angle_1_deg	6.19
r_scangle_it	4.024
r_scbond_it	2.578
r_angle_refined_deg	1.521
r_mcangle_it	1.478
r_angle_other_deg	0.874
r_mcbond_it	0.802
r_mcbond_other	0.173
r_chiral_restr	0.079
r_bond_refined_d	0.015
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3084
Nucleic Acid Atoms
Solvent Atoms	216
Heterogen Atoms	20

Software

Software
Software Name	Purpose
SHARP	phasing
PARROT	phasing
ARP/wARP	model building
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling