1O8B

Structure of Escherichia coli ribose-5-phosphate isomerase, RpiA, complexed with arabinose-5-phosphate.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1KS2PDB ENTRY 1KS2

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.5CRYSTALS WERE GROWN FROM A SOLUTION CONTAINING 3.5 MG/ML PROTEIN, 30-35 % PEG 4000 10 MM ARABINOSE-5-PHOSPHATE, 0.05M TRIS-HCL PH 8.4, 0.1 M MGCL2
Crystal Properties
Matthews coefficientSolvent content
2.346

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.049α = 90.23
b = 42.4β = 100.98
c = 60.195γ = 98.98
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDGE(220),HORIZONTAL FOCUSING MULTILAYER2002-07-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-1ESRFID14-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.254081.80.09512.44.390067
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.251.3240.10.761.13.6

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 1KS21.254086708449881.80.2240.2240.24RANDOM10.26
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]
-0.54-0.680.25-0.48-0.30.89
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it3.122
r_scbond_it2.236
r_angle_other_deg1.863
r_mcangle_it1.147
r_mcbond_it0.775
r_symmetry_hbond_refined0.507
r_nbd_refined0.22
r_symmetry_vdw_refined0.161
r_xyhbond_nbd_refined0.116
r_chiral_restr0.108
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it3.122
r_scbond_it2.236
r_angle_other_deg1.863
r_mcangle_it1.147
r_mcbond_it0.775
r_symmetry_hbond_refined0.507
r_nbd_refined0.22
r_symmetry_vdw_refined0.161
r_xyhbond_nbd_refined0.116
r_chiral_restr0.108
r_bond_refined_d0.016
r_gen_planes_refined0.008
r_bond_other_d
r_angle_refined_deg
r_dihedral_angle_1_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_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 Atoms2771
Nucleic Acid Atoms
Solvent Atoms159
Heterogen Atoms28

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing