3PH4

Clostridium thermocellum Ribose-5-Phosphate Isomerase B with d-allose


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3HE8 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52850.05M Tris pH 7.0, 10% PEG 8000, 0.15M Magnesium chloride, 0.2M Potassium chloride , VAPOR DIFFUSION, SITTING DROP, temperature 285K
Crystal Properties
Matthews coefficientSolvent content
2.957.65

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.134α = 90
b = 69.134β = 90
c = 154.284γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102009-10-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPAL/PLS BEAMLINE 6C11.24PAL/PLS6C1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.075095.72567325673-2-2
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.12.299.3

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 REPLACEMENTTHROUGHOUT3HE82.0739.012510625106133398.670.185990.185990.18420.22004RANDOM33.192
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]
0.010.01-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.66
r_dihedral_angle_4_deg17.851
r_dihedral_angle_3_deg13.749
r_dihedral_angle_1_deg6.069
r_scangle_it5.662
r_scbond_it3.697
r_mcangle_it2.082
r_angle_refined_deg2.018
r_mcbond_it1.194
r_chiral_restr0.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.66
r_dihedral_angle_4_deg17.851
r_dihedral_angle_3_deg13.749
r_dihedral_angle_1_deg6.069
r_scangle_it5.662
r_scbond_it3.697
r_mcangle_it2.082
r_angle_refined_deg2.018
r_mcbond_it1.194
r_chiral_restr0.16
r_bond_refined_d0.026
r_gen_planes_refined0.009
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2244
Nucleic Acid Atoms
Solvent Atoms176
Heterogen Atoms24

Software

Software
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling