2CIR

Structure-based functional annotation: Yeast ymr099c codes for a D- hexose-6-phosphate mutarotase. Complex with glucose-6-phosphate


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.532% POLYETHYLENE GLYCOL 4000, 0.2 M LITHIUM CHLORIDE, 0.1M HEPES PH 7.5.
Crystal Properties
Matthews coefficientSolvent content
2.850

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.63α = 90
b = 157.067β = 90
c = 104.024γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2005-11-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-1ESRFID14-1

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
11.52098.90.0821.54.3578462
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)
11.51.699.60.462.5

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 2CIQ1.62044062237697.50.2080.2060.234RANDOM21.96
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]
1.62-1.21-0.41
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.154
r_dihedral_angle_3_deg13.303
r_dihedral_angle_4_deg12.227
r_dihedral_angle_1_deg6.162
r_scangle_it3.404
r_scbond_it2.753
r_mcangle_it1.668
r_angle_refined_deg1.307
r_mcbond_it1.095
r_nbtor_refined0.309
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.154
r_dihedral_angle_3_deg13.303
r_dihedral_angle_4_deg12.227
r_dihedral_angle_1_deg6.162
r_scangle_it3.404
r_scbond_it2.753
r_mcangle_it1.668
r_angle_refined_deg1.307
r_mcbond_it1.095
r_nbtor_refined0.309
r_nbd_refined0.195
r_xyhbond_nbd_refined0.129
r_symmetry_vdw_refined0.129
r_chiral_restr0.091
r_symmetry_hbond_refined0.087
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
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 Atoms2321
Nucleic Acid Atoms
Solvent Atoms252
Heterogen Atoms16

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing