2AFB | pdb_00002afb

Crystal structure of 2-dehydro-3- deoxygluconokinase (EC 2.7.1.45) (tm0067) from THERMOTOGA MARITIMA at 2.05 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION,SITTING DROP,NANODROP	7	273	50.0% PEG-200, 0.1M Tris pH 7.0 , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 273K

Crystal Properties
Matthews coefficient	Solvent content
2.41	48.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 120.993	α = 90
b = 120.993	β = 90
c = 260.3	γ = 120

Symmetry
Space Group	H 3 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	ADSC QUANTUM 4		2001-07-01	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.979413, 0.904964, 0.979150	SSRL	BL9-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.05	49.69	98.2	0.077	0.077	6.6	4.6		45533			27.8

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	2.05	2.16	89.9	89.9	0.381	0.381	1.9	2.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	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	MAD	THROUGHOUT	2.05	48.63	44437	1069	98.07	0.177	0.177	0.176	0.19	0.23	0.24	RANDOM	28.282

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]
0.74	0.37		0.74		-1.12

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.363
r_dihedral_angle_3_deg	15.112
r_dihedral_angle_4_deg	14.239
r_dihedral_angle_1_deg	6.892
r_scangle_it	6.783
r_scbond_it	5.306
r_mcangle_it	2.974
r_mcbond_it	2.202
r_angle_refined_deg	1.55
r_angle_other_deg	0.835
r_mcbond_other	0.708
r_symmetry_vdw_refined	0.415
r_symmetry_vdw_other	0.35
r_symmetry_metal_ion_refined	0.348
r_metal_ion_refined	0.306
r_nbd_refined	0.211
r_nbtor_refined	0.183
r_nbd_other	0.178
r_xyhbond_nbd_refined	0.152
r_symmetry_hbond_refined	0.12
r_chiral_restr	0.093
r_nbtor_other	0.086
r_bond_refined_d	0.018
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5040
Nucleic Acid Atoms
Solvent Atoms	394
Heterogen Atoms	10

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
CCP4	data scaling
SnB	phasing
MLPHARE	phasing
CCP4	phasing
SOLVE	phasing
SHARP	phasing