3O6Z

Structure of the D152A E.coli GDP-mannose hydrolase (yffh) in complex with Mg++


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3O52PDB entry 3O52

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.529120-26% PEG 3350, 0.2 M MgCl2, 0.1 M Tris pH 8.5, 4 mM GDP-mannose at a ratio of 1:1 protein:reservoir, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.3447.34

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.916α = 90
b = 69.333β = 90
c = 99.612γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2009-07-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E+ DW1.54

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
12.0320.47980.07716.66.126521
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)
2.032.198.10.3745.62608

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 3O522.0520.4725302128096.230.23830.23470.3033RANDOM34.263
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]
1.92-0.91-1.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.408
r_dihedral_angle_3_deg15.657
r_dihedral_angle_4_deg15.61
r_dihedral_angle_1_deg6.561
r_scangle_it2.634
r_scbond_it1.819
r_angle_refined_deg1.438
r_mcangle_it1.226
r_mcbond_it0.777
r_nbtor_refined0.303
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.408
r_dihedral_angle_3_deg15.657
r_dihedral_angle_4_deg15.61
r_dihedral_angle_1_deg6.561
r_scangle_it2.634
r_scbond_it1.819
r_angle_refined_deg1.438
r_mcangle_it1.226
r_mcbond_it0.777
r_nbtor_refined0.303
r_symmetry_vdw_refined0.273
r_symmetry_hbond_refined0.226
r_nbd_refined0.206
r_xyhbond_nbd_refined0.174
r_chiral_restr0.092
r_metal_ion_refined0.049
r_bond_refined_d0.014
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2969
Nucleic Acid Atoms
Solvent Atoms329
Heterogen Atoms27

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
AMoREphasing