1RYA

Crystal Structure of the E. coli GDP-mannose mannosyl hydrolase in complex with GDP and MG


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.529320% PEG 4000, 0.2M Na (or Mg) Acetate, 0.1M Tris HCl pH8.5), VAPOR DIFFUSION, SITTING DROP
Crystal Properties
Matthews coefficientSolvent content
2.7355.02

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.069α = 90
b = 81.363β = 90
c = 98.974γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray180CCDADSC QUANTUM 4MSINGLE WAVELENGTH
21IMAGE PLATERIGAKU RAXIS IV
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X6A0.9791NSLSX6A
2ROTATING ANODERIGAKU RU2001.54

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.363.2592.410.09338.28814388143
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.2981.33273.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONMIRTHROUGHOUT1.363.2588143471592.410.169940.168820.19059RANDOM11.643
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]
0.26-0.23-0.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.737
r_scangle_it3.016
r_scbond_it1.967
r_angle_refined_deg1.557
r_mcangle_it1.416
r_angle_other_deg0.847
r_mcbond_it0.77
r_symmetry_vdw_other0.367
r_nbd_other0.261
r_nbd_refined0.217
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.737
r_scangle_it3.016
r_scbond_it1.967
r_angle_refined_deg1.557
r_mcangle_it1.416
r_angle_other_deg0.847
r_mcbond_it0.77
r_symmetry_vdw_other0.367
r_nbd_other0.261
r_nbd_refined0.217
r_symmetry_hbond_refined0.19
r_xyhbond_nbd_refined0.146
r_symmetry_vdw_refined0.145
r_chiral_restr0.088
r_nbtor_other0.081
r_gen_planes_other0.016
r_gen_planes_refined0.011
r_bond_refined_d0.01
r_bond_other_d0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2606
Nucleic Acid Atoms
Solvent Atoms727
Heterogen Atoms75

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
AMoREphasing