4BKP | pdb_00004bkp

Crystal structure of human GDP-L-fucose synthase with bound NADP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4B8WPDB ENTRY 4B8W

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
120% PEG 3350, 0.1M CITRATE PH 5.5
Crystal Properties
Matthews coefficientSolvent content
2.8556.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 106.596α = 90
b = 163.095β = 90
c = 197.581γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2012-12-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I03DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.749.41000.114.96.8476051.9
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.72.7999.91.071.96.9

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 4B8W2.749.4445196240899.950.19780.196030.20.230910.23RANDOM63.195
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]
0.940.47-1.4
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.989
r_dihedral_angle_4_deg15.904
r_dihedral_angle_3_deg15.524
r_mcangle_it7.215
r_scbond_it6.098
r_dihedral_angle_1_deg5.228
r_mcbond_it5.044
r_mcbond_other5.042
r_angle_refined_deg1.198
r_angle_other_deg0.868
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.989
r_dihedral_angle_4_deg15.904
r_dihedral_angle_3_deg15.524
r_mcangle_it7.215
r_scbond_it6.098
r_dihedral_angle_1_deg5.228
r_mcbond_it5.044
r_mcbond_other5.042
r_angle_refined_deg1.198
r_angle_other_deg0.868
r_chiral_restr0.062
r_bond_refined_d0.007
r_gen_planes_refined0.005
r_bond_other_d0.003
r_gen_planes_other0.003
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_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9797
Nucleic Acid Atoms
Solvent Atoms50
Heterogen Atoms209

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing