6GPJ

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1T2A 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29320% PEG3350 -- 0.2M ammonium citrate dibasic
Crystal Properties
Matthews coefficientSolvent content
2.3848.37

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.08α = 90
b = 114.438β = 90
c = 140.536γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2017-03-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I240.96860DiamondI24

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.9463.911005.86.5110446
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.941.991001.26.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT1T2A1.9463.9104361530899.260.211040.209670.23847RANDOM27.493
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]
-0.811.82-1.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.702
r_dihedral_angle_4_deg17.105
r_dihedral_angle_3_deg12.972
r_dihedral_angle_1_deg6.037
r_long_range_B_refined4.693
r_long_range_B_other4.683
r_scangle_other3.304
r_mcangle_it2.559
r_mcangle_other2.559
r_scbond_it2.117
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.702
r_dihedral_angle_4_deg17.105
r_dihedral_angle_3_deg12.972
r_dihedral_angle_1_deg6.037
r_long_range_B_refined4.693
r_long_range_B_other4.683
r_scangle_other3.304
r_mcangle_it2.559
r_mcangle_other2.559
r_scbond_it2.117
r_scbond_other2.113
r_mcbond_it1.71
r_mcbond_other1.709
r_angle_refined_deg1.482
r_angle_other_deg0.944
r_chiral_restr0.083
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.001
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10832
Nucleic Acid Atoms
Solvent Atoms736
Heterogen Atoms382

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing