2QH5

Crystal structure of mannose-6-phosphate isomerase from Helicobacter pylori


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.52940.1M Bis-tris, 25% PEG 3350, 0.2M Sodium chloride, pH 5.5, 10% Glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
2.2645.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.829α = 90
b = 66.415β = 90
c = 163.959γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mmMIRRORS2007-06-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 31-ID0.97960APS31-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.35099.80.0890.0594.54.6289102891055.06
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.3899.20.770.630.83.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)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 DIFFRACTIONSADTHROUGHOUT2.320278122781293199.870.235210.235210.23350.289RANDOM69.524
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]
3.591.26-4.86
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.177
r_dihedral_angle_4_deg20.94
r_dihedral_angle_3_deg19.571
r_scangle_it8.244
r_dihedral_angle_1_deg6.107
r_scbond_it5.787
r_mcangle_it5.52
r_mcbond_it3.52
r_angle_refined_deg1.173
r_nbtor_refined0.314
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.177
r_dihedral_angle_4_deg20.94
r_dihedral_angle_3_deg19.571
r_scangle_it8.244
r_dihedral_angle_1_deg6.107
r_scbond_it5.787
r_mcangle_it5.52
r_mcbond_it3.52
r_angle_refined_deg1.173
r_nbtor_refined0.314
r_symmetry_hbond_refined0.197
r_xyhbond_nbd_refined0.194
r_nbd_refined0.17
r_symmetry_vdw_refined0.142
r_chiral_restr0.087
r_bond_refined_d0.007
r_gen_planes_refined0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4079
Nucleic Acid Atoms
Solvent Atoms96
Heterogen Atoms

Software

Software
Software NamePurpose
SHELXmodel building
REFMACrefinement
MAR345data collection
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing