Experiment: 3CM0

Crystal structure of adenylate kinase from Thermus thermophilus HB8

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2AK2	PDB ENTRY 2AK2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	4.5	293	40% 1,2-propanediol, 0.1M NaAcetate, pH4.5, VAPOR DIFFUSION, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.42	49.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.446	α = 90
b = 51.446	β = 90
c = 131.474	γ = 120

Symmetry
Space Group	P 32 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	90	IMAGE PLATE	RIGAKU RAXIS V		2003-03-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL45PX	1.0000	SPring-8	BL45PX

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	1.8	50	99.5	0.068				19365		1	18.8

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)
	1.8	1.86	100		0.243

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2AK2	1.8	44.55	19365	19109	1888	98.3	0.205	0.205	0.2088	0.242	0.2125	RANDOM	27.6

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]
-0.86			-0.86		1.71

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	20.7
c_angle_deg	1.4
c_improper_angle_d	0.91
c_bond_d	0.013

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1445
Nucleic Acid Atoms
Solvent Atoms	88
Heterogen Atoms

Software

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