2I8T

GDP-mannose mannosyl hydrolase-calcium-GDP-mannose complex


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP828110-20% PEG 4000 200 mM sodium acetate 100 mM HEPES, pH 8.0 harvested immediately after growth, VAPOR DIFFUSION, HANGING DROP, temperature 281K
Crystal Properties
Matthews coefficientSolvent content
2.5752.16

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.636α = 90
b = 81.586β = 90
c = 98.3γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1.00APS22-ID

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
11.35095.80.04294945851
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)
11.31.3581.20.14947936

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.342.419452668061000.1530.1530.1510.174RANDOM8.43
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]
0.29-0.09-0.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.391
r_sphericity_free19.806
r_dihedral_angle_4_deg13.54
r_dihedral_angle_3_deg11.016
r_dihedral_angle_1_deg4.82
r_sphericity_bonded1.705
r_angle_refined_deg1.703
r_scangle_it1.586
r_mcangle_it1.298
r_scbond_it1.112
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.391
r_sphericity_free19.806
r_dihedral_angle_4_deg13.54
r_dihedral_angle_3_deg11.016
r_dihedral_angle_1_deg4.82
r_sphericity_bonded1.705
r_angle_refined_deg1.703
r_scangle_it1.586
r_mcangle_it1.298
r_scbond_it1.112
r_angle_other_deg1.035
r_mcbond_it0.875
r_rigid_bond_restr0.469
r_symmetry_vdw_other0.357
r_nbd_other0.192
r_nbd_refined0.186
r_nbtor_refined0.186
r_mcbond_other0.146
r_xyhbond_nbd_refined0.143
r_symmetry_hbond_refined0.138
r_metal_ion_refined0.114
r_symmetry_vdw_refined0.098
r_chiral_restr0.095
r_nbtor_other0.083
r_gen_planes_refined0.003
r_bond_refined_d0.002
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2448
Nucleic Acid Atoms
Solvent Atoms593
Heterogen Atoms92

Software

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