2X5Z

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
14.6100 MM SODIUM ACETATE PH 5.0, 30% (V/V) MPD, 20 MM CALCIUM CHLORIDE
Crystal Properties
Matthews coefficientSolvent content
2.7455.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 84.227α = 90
b = 96.035β = 90
c = 217.122γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2009-04-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-4ESRFID14-4

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
12.75099.80.0524.45.724606365.6
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)
12.72.8599.90.444.25.8

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 2X5S2.75023310125799.770.193740.191110.24415RANDOM63.553
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]
0.21-0.720.51
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.772
r_dihedral_angle_3_deg16.921
r_dihedral_angle_4_deg15.155
r_dihedral_angle_1_deg6.069
r_scangle_it2.737
r_scbond_it1.634
r_angle_refined_deg1.457
r_mcangle_it1.052
r_angle_other_deg0.859
r_mcbond_it0.541
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.772
r_dihedral_angle_3_deg16.921
r_dihedral_angle_4_deg15.155
r_dihedral_angle_1_deg6.069
r_scangle_it2.737
r_scbond_it1.634
r_angle_refined_deg1.457
r_mcangle_it1.052
r_angle_other_deg0.859
r_mcbond_it0.541
r_mcbond_other0.101
r_chiral_restr0.077
r_bond_refined_d0.013
r_gen_planes_refined0.006
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 Atoms5396
Nucleic Acid Atoms
Solvent Atoms38
Heterogen Atoms79

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing