2X5S

Crystal structure of T. maritima GDP-mannose pyrophosphorylase in apo state.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2CU2PDB ENTRY 2CU2

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5100 MM PCB PH 7.5, 35% (V/V) MPD
Crystal Properties
Matthews coefficientSolvent content
2.4349.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.011α = 90
b = 92.999β = 110.25
c = 69.687γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2007-03-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID29ESRFID29

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
12.3565.3799.20.05523.56317443.559.338
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)
12.352.4896.90.472.55.4

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 2CU22.3565.3730129160299.130.226480.223850.27315RANDOM75.786
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]
-4.181.184.940.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.133
r_dihedral_angle_3_deg15.661
r_dihedral_angle_4_deg14.452
r_dihedral_angle_1_deg5.911
r_scangle_it2.008
r_scbond_it1.217
r_angle_refined_deg1.154
r_mcangle_it0.797
r_angle_other_deg0.787
r_mcbond_it0.416
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.133
r_dihedral_angle_3_deg15.661
r_dihedral_angle_4_deg14.452
r_dihedral_angle_1_deg5.911
r_scangle_it2.008
r_scbond_it1.217
r_angle_refined_deg1.154
r_mcangle_it0.797
r_angle_other_deg0.787
r_mcbond_it0.416
r_mcbond_other0.073
r_chiral_restr0.064
r_bond_refined_d0.01
r_gen_planes_refined0.004
r_bond_other_d0.002
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 Atoms5367
Nucleic Acid Atoms
Solvent Atoms47
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing