2GLK

High-resolution study of D-Xylose isomerase, 0.94A resolution.


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION829350mM tris-HCl,25%AMSO4,2mM Mn2+ and 2mM Co2+ , XI @ 25mg/ml., pH 8, VAPOR DIFFUSION, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.6753.93

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.712α = 90
b = 97.935β = 90
c = 101.867γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2001-09-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 17-ID1.0APS17-ID

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
10.9435.3685.6252079252079
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
10.9440.96512

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 REPLACEMENTTHROUGHOUT1XIB0.9435.362520792310372104285.590.11570.11570.114580.12792RANDOM11.123
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]
0.21-0.11-0.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.824
r_dihedral_angle_4_deg13.787
r_dihedral_angle_3_deg12.414
r_sphericity_free11.867
r_sphericity_bonded5.914
r_dihedral_angle_1_deg5.472
r_scangle_it4.695
r_scbond_it3.436
r_mcangle_it2.56
r_mcbond_it2.118
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.824
r_dihedral_angle_4_deg13.787
r_dihedral_angle_3_deg12.414
r_sphericity_free11.867
r_sphericity_bonded5.914
r_dihedral_angle_1_deg5.472
r_scangle_it4.695
r_scbond_it3.436
r_mcangle_it2.56
r_mcbond_it2.118
r_angle_refined_deg1.917
r_angle_other_deg1.869
r_rigid_bond_restr1.842
r_mcbond_other1.316
r_symmetry_vdw_other0.34
r_symmetry_vdw_refined0.3
r_nbd_refined0.235
r_symmetry_hbond_refined0.207
r_nbd_other0.205
r_nbtor_refined0.19
r_xyhbond_nbd_refined0.176
r_chiral_restr0.112
r_nbtor_other0.095
r_bond_refined_d0.021
r_gen_planes_refined0.012
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3054
Nucleic Acid Atoms
Solvent Atoms426
Heterogen Atoms26

Software

Software
Software NamePurpose
REFMACrefinement
X-GENdata reduction
HKL-2000data scaling
AMoREphasing