6GPK

Crystal structure of human GDP-D-mannose 4,6-dehydratase (E157Q) in complex with GDP-Man

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	20% PEG3350, 0.15M DL- malic acid

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.73	α = 90
b = 114.532	β = 90
c = 140.061	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M		2017-05-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.92819	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.47	140.06	100	17.2	6.7		254599

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.47	1.55			2.5

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION		THROUGHOUT	1.47	88.66	241686	12794	99.96	0.14226	0.14056	0.17434	RANDOM	23.674

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]
-0.82			1.9		-1.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.574
r_sphericity_free	27.232
r_dihedral_angle_4_deg	14.095
r_dihedral_angle_3_deg	12.157
r_sphericity_bonded	11.465
r_dihedral_angle_1_deg	6.119
r_long_range_B_refined	3.642
r_long_range_B_other	3.642
r_scangle_other	2.683
r_mcangle_it	2.379
r_mcangle_other	2.379
r_scbond_it	2.12
r_scbond_other	2.12
r_rigid_bond_restr	1.817
r_mcbond_it	1.814
r_mcbond_other	1.812
r_angle_refined_deg	1.505
r_angle_other_deg	0.975
r_chiral_restr	0.091
r_bond_refined_d	0.013
r_gen_planes_refined	0.007
r_bond_other_d	0.002
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_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10903
Nucleic Acid Atoms
Solvent Atoms	858
Heterogen Atoms	466

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing