1X7N

The crystal structure of Pyrococcus furiosus phosphoglucose isomerase with bound 5-phospho-D-arabinonate and Manganese


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1PLZ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52931.6M tri-sodium citrate, 50mM 5-phospho-D-arabinonate, 100mM MnCl2, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
1.935.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 84.674α = 90
b = 42.382β = 120.57
c = 57.255γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCHyale mirrors2003-08-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.54

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
11.8949.3997.90.0524.531372613726
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)
11.891.9481.30.3492.792.3741

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 REPLACEMENTTHROUGHOUT1PLZ1.8949.391307565196.970.14390.14390.140510.21226RANDOM30.619
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]
-0.13-0.190.26-0.33
RMS Deviations
KeyRefinement Restraint Deviation
r_scbond_it31.869
r_scangle_it28.127
r_mcangle_it14.296
r_mcbond_it12.569
r_dihedral_angle_1_deg7.053
r_angle_refined_deg1.354
r_angle_other_deg0.739
r_symmetry_vdw_other0.269
r_nbd_other0.239
r_nbd_refined0.201
RMS Deviations
KeyRefinement Restraint Deviation
r_scbond_it31.869
r_scangle_it28.127
r_mcangle_it14.296
r_mcbond_it12.569
r_dihedral_angle_1_deg7.053
r_angle_refined_deg1.354
r_angle_other_deg0.739
r_symmetry_vdw_other0.269
r_nbd_other0.239
r_nbd_refined0.201
r_symmetry_hbond_refined0.145
r_xyhbond_nbd_refined0.135
r_symmetry_vdw_refined0.133
r_chiral_restr0.082
r_nbtor_other0.082
r_bond_refined_d0.011
r_gen_planes_refined0.005
r_gen_planes_other0.003
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1519
Nucleic Acid Atoms
Solvent Atoms205
Heterogen Atoms16

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing