2WHE

Structure of native Beta-Phosphoglucomutase in an open conformation without bound ligands.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1ZOLPDB ENTRY 1ZOL

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.228-29 % PEG 4000 AND 200 MM NA ACETATE, pH 7.2
Crystal Properties
Matthews coefficientSolvent content
2.0238.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.239α = 90
b = 56.9β = 90
c = 75.441γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDGE2112007-09-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-2ESRFID14-2

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
11.5543.584.30.0610.72.428532319.2
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)
11.551.6343.10.342.12

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 1ZOL1.5520270341454840.1770.1760.208RANDOM14.34
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]
0.66-0.36-0.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.262
r_dihedral_angle_3_deg14.295
r_dihedral_angle_4_deg13.493
r_dihedral_angle_1_deg5.56
r_scangle_it5.458
r_scbond_it3.203
r_mcangle_it1.894
r_angle_refined_deg1.686
r_mcbond_it1.089
r_angle_other_deg1.008
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.262
r_dihedral_angle_3_deg14.295
r_dihedral_angle_4_deg13.493
r_dihedral_angle_1_deg5.56
r_scangle_it5.458
r_scbond_it3.203
r_mcangle_it1.894
r_angle_refined_deg1.686
r_mcbond_it1.089
r_angle_other_deg1.008
r_mcbond_other0.343
r_chiral_restr0.108
r_bond_refined_d0.02
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
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_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 Atoms1708
Nucleic Acid Atoms
Solvent Atoms309
Heterogen Atoms1

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing