2C5A

GDP-mannose-3', 5' -epimerase (Arabidopsis thaliana),Y174F, with GDP-beta-L-galactose bound in the active site


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2C54PDB ENTRY 2C54

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6100 MM BIS-TRIS PH 6.0, 2.2M AMMONIUM SULPHATE, SITTING DROP, VAPOUR DIFFUSION. CRYOPROTECTED 6 M SODIUM FORMATE.
Crystal Properties
Matthews coefficientSolvent content
1.9938.16

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.497α = 90
b = 83.273β = 98.89
c = 66.12γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2005-05-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-2ESRFID14-2

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
11.423.1296.70.0517.93.612682611
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)
11.41.4895.40.235.53.5

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2C541.421.61126798633796.50.1050.1030.14RANDOM9.78
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]
-0.262-0.050.589-0.342
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.509
r_dihedral_angle_4_deg21.328
r_dihedral_angle_3_deg12.532
r_dihedral_angle_1_deg6.407
r_scangle_it4.774
r_scbond_it3.673
r_mcangle_it2.518
r_mcbond_it2.188
r_angle_refined_deg1.921
r_angle_other_deg1.086
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.509
r_dihedral_angle_4_deg21.328
r_dihedral_angle_3_deg12.532
r_dihedral_angle_1_deg6.407
r_scangle_it4.774
r_scbond_it3.673
r_mcangle_it2.518
r_mcbond_it2.188
r_angle_refined_deg1.921
r_angle_other_deg1.086
r_symmetry_vdw_other0.283
r_nbd_refined0.23
r_xyhbond_nbd_refined0.227
r_symmetry_hbond_refined0.225
r_chiral_restr0.217
r_nbd_other0.208
r_symmetry_vdw_refined0.191
r_nbtor_refined0.186
r_nbtor_other0.089
r_bond_refined_d0.02
r_gen_planes_refined0.01
r_bond_other_d0.002
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
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 Atoms5786
Nucleic Acid Atoms
Solvent Atoms1018
Heterogen Atoms231

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling