2GC0

The crystal structure of phosphoglucose isomerase from Pyrococcus furiosus in complex with 5-phospho-D-arabinonohydroxamate and zinc


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1X8EPDB ENTRY 1X8E

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52900.1 M tri sodium citrate pH 6.5, 30% polyethylene glycol 4000 and 10% isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
2.1342.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.149α = 90
b = 73.112β = 90
c = 74.159γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCHOsmic Varimax2005-03-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007

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
1274.15999.70.1160.1165.64.6252492524917.6
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)
22.1199.499.40.420.421.84.53597

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1X8E217.412524925249128999.810.1690.1690.1660.241RANDOM20.189
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]
-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.761
r_dihedral_angle_3_deg15.366
r_dihedral_angle_4_deg13.976
r_scangle_it10.567
r_scbond_it8.305
r_mcangle_it7.286
r_dihedral_angle_1_deg6.652
r_mcbond_it6.523
r_angle_refined_deg1.216
r_nbtor_refined0.306
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.761
r_dihedral_angle_3_deg15.366
r_dihedral_angle_4_deg13.976
r_scangle_it10.567
r_scbond_it8.305
r_mcangle_it7.286
r_dihedral_angle_1_deg6.652
r_mcbond_it6.523
r_angle_refined_deg1.216
r_nbtor_refined0.306
r_symmetry_vdw_refined0.299
r_symmetry_hbond_refined0.2
r_nbd_refined0.184
r_xyhbond_nbd_refined0.132
r_chiral_restr0.081
r_bond_refined_d0.009
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3020
Nucleic Acid Atoms
Solvent Atoms336
Heterogen Atoms34

Software

Software
Software NamePurpose
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
CCP4data scaling