2Z1M

Crystal Structure of GDP-D-Mannose Dehydratase from Aquifex aeolicus VF5

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.2	293	0.2M Sodium chloride , 0.1M NA/K PHOSPHATE, 40% PEG 400, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.799	α = 90
b = 151.164	β = 108.6
c = 85.934	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	RIGAKU JUPITER 210		2006-10-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL26B2	1.000	SPring-8	BL26B2

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	50	99	0.074	19.6	4.9	94553	94553			24.4

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	2	2.07	93		0.209	5.4	3.4	8849

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2	50	89779	89779	4740	98.8	0.2	0.2	0.198	0.233	RANDOM	26.383

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]
0.17		-0.19	-1.67		1.38

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.885
r_dihedral_angle_4_deg	16.262
r_dihedral_angle_3_deg	13.408
r_dihedral_angle_1_deg	5.519
r_scangle_it	2.413
r_scbond_it	1.604
r_angle_refined_deg	1.187
r_mcangle_it	1.061
r_mcbond_it	0.645
r_nbtor_refined	0.306
r_symmetry_vdw_refined	0.199
r_nbd_refined	0.193
r_symmetry_hbond_refined	0.141
r_xyhbond_nbd_refined	0.132
r_chiral_restr	0.082
r_bond_refined_d	0.01
r_gen_planes_refined	0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10725
Nucleic Acid Atoms
Solvent Atoms	516
Heterogen Atoms	152

Software

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