1S3G

Crystal structure of adenylate kinase from Bacillus globisporus

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1P3J	PDB ENTRY 1P3J

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	small-scale batch method	7	293	ammonium sulfate, PEG 1000, sodium azide, pH 7.0, small-scale batch method, temperature 293.0K

Crystal Properties
Matthews coefficient	Solvent content
2.38	47.93

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.288	α = 90
b = 65.288	β = 90
c = 94.378	γ = 120

Symmetry
Space Group	P 31 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	MAR CCD 165 mm		2003-07-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 14-ID-B	1.1271	APS	14-ID-B

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	2.25	50	99.2	0.057	24.6	5.2		21054			32.6

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)
	2.25	2.33	99.4		0.593	2.5	4.6	1112

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1P3J	2.25	27.49	19702	19702	1739	92.5	0.223	0.223	0.288	RANDOM	51.5

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]
-1.65	1.98		-1.65		3.3

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	20.8
c_scangle_it	6.28
c_scbond_it	5.15
c_mcangle_it	2.55
c_mcbond_it	1.61
c_angle_deg	1.2
c_improper_angle_d	0.82
c_bond_d	0.017
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1684
Nucleic Acid Atoms
Solvent Atoms	109
Heterogen Atoms	58

Software

Software
Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
SOMORE	phasing