2IPN

Crystal structure of a disulfide mutant glucose binding protein


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2HPH 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.529020% PEG 6000, 50mM HEPES, pH7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
2.0239.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.305α = 90
b = 36.586β = 106.92
c = 65.029γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42006-06-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.1ALS8.2.1

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
11.155099.50.06311.83.39750697506
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)
1.151.1997.90.2843.32.59495

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 REPLACEMENTTHROUGHOUT2HPH1.15509747897478487599.410.1530.1530.1530.168RANDOM7.754
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]
0.070.12-0.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.111
r_dihedral_angle_3_deg11.226
r_dihedral_angle_4_deg8.562
r_dihedral_angle_1_deg5.371
r_sphericity_free3.803
r_scangle_it2.555
r_sphericity_bonded2.079
r_scbond_it1.777
r_mcangle_it1.25
r_angle_refined_deg1.244
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.111
r_dihedral_angle_3_deg11.226
r_dihedral_angle_4_deg8.562
r_dihedral_angle_1_deg5.371
r_sphericity_free3.803
r_scangle_it2.555
r_sphericity_bonded2.079
r_scbond_it1.777
r_mcangle_it1.25
r_angle_refined_deg1.244
r_angle_other_deg0.881
r_mcbond_it0.873
r_rigid_bond_restr0.788
r_mcbond_other0.333
r_symmetry_vdw_other0.231
r_symmetry_vdw_refined0.227
r_nbd_refined0.215
r_nbd_other0.175
r_nbtor_refined0.173
r_symmetry_hbond_refined0.124
r_xyhbond_nbd_refined0.113
r_metal_ion_refined0.087
r_nbtor_other0.085
r_chiral_restr0.077
r_bond_refined_d0.007
r_gen_planes_refined0.005
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2469
Nucleic Acid Atoms
Solvent Atoms361
Heterogen Atoms13

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
HKL-2000data reduction
AMoREphasing