1O1X

Crystal structure of a ribose 5-phosphate isomerase rpib (tm1080) from thermotoga maritima at 1.90 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1727740 % (+/-)-2-Methyl-2,4-Pentanediol; 0.1 M HEPES pH 7.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K, pH 7.00
Crystal Properties
Matthews coefficientSolvent content
2.5651.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.49α = 90
b = 73.89β = 90
c = 87.74γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4FLAT MIRROR,SINGLE CRYSTAL SI(311) BENT MONOCHROMATOR2002-11-26MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-10.91837, 0.97931, 0.97892SSRLBL9-1

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
11.929.78899.10.067154.715973
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)
11.91.9593.20.2843.42.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONMADTHROUGHOUT1.928.26151688031000.1180.1170.138random13.98
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]
1.4-1.1-0.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.571
r_dihedral_angle_4_deg15.732
r_dihedral_angle_3_deg11.572
r_dihedral_angle_1_deg5.529
r_scangle_it4.246
r_scbond_it2.562
r_angle_refined_deg1.518
r_mcangle_it1.467
r_angle_other_deg0.934
r_mcbond_it0.772
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.571
r_dihedral_angle_4_deg15.732
r_dihedral_angle_3_deg11.572
r_dihedral_angle_1_deg5.529
r_scangle_it4.246
r_scbond_it2.562
r_angle_refined_deg1.518
r_mcangle_it1.467
r_angle_other_deg0.934
r_mcbond_it0.772
r_symmetry_vdw_other0.308
r_symmetry_hbond_refined0.259
r_xyhbond_nbd_refined0.24
r_nbd_other0.239
r_nbd_refined0.217
r_symmetry_vdw_refined0.178
r_chiral_restr0.1
r_nbtor_other0.084
r_bond_refined_d0.016
r_gen_planes_refined0.008
r_bond_other_d0.006
r_gen_planes_other0.001
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1139
Nucleic Acid Atoms
Solvent Atoms212
Heterogen Atoms8

Software

Software
Software NamePurpose
REFMACrefinement
SCALAdata scaling
RESOLVEmodel building
SOLVEphasing
CNSrefinement
MOSFLMdata reduction
XFITdata reduction
CCP4data scaling
RESOLVEphasing