2X60

Crystal structure of T. maritima GDP-mannose pyrophosphorylase in complex with GTP.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2X5SPDB ENTRY 2X5S

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15100 MM SODIUM ACETATE PH 5.0, 30% (V/V) MPD, 200 MM CALCIUM CHLORIDE
Crystal Properties
Matthews coefficientSolvent content
2.2244.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.926α = 90
b = 79.567β = 107.75
c = 70.952γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2009-03-14MSINGLE 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
12.867.698.90.06163.117147366.9
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)
12.82.9599.10.482.63.1

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 2X5S2.867.5716126100798.720.211040.207370.26697RANDOM74.769
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]
0.593.163.56-2.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.415
r_dihedral_angle_3_deg16.371
r_dihedral_angle_4_deg15.414
r_dihedral_angle_1_deg5.934
r_scangle_it1.462
r_angle_refined_deg1.218
r_scbond_it0.857
r_angle_other_deg0.813
r_mcangle_it0.533
r_mcbond_it0.279
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.415
r_dihedral_angle_3_deg16.371
r_dihedral_angle_4_deg15.414
r_dihedral_angle_1_deg5.934
r_scangle_it1.462
r_angle_refined_deg1.218
r_scbond_it0.857
r_angle_other_deg0.813
r_mcangle_it0.533
r_mcbond_it0.279
r_chiral_restr0.068
r_mcbond_other0.049
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_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 Atoms5380
Nucleic Acid Atoms
Solvent Atoms19
Heterogen Atoms66

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing