2GUC

Crystal structure of a complex of griffithsin with mannose at 1.78 A resolution.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2GTYPDB ENTRY 2GTY

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52931.8M magnesium sulfate, 0.1M MES, 1:10 ratio of griffithsin monomers to mannose, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.3848.43

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.77α = 90
b = 39.46β = 91
c = 57.24γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plate2006-02-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU

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
11.785093.30.04137.24.42173921739-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.781.8473.7

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2GTY1.79302173921726110894.140.15070.15070.15070.1887RANDOM17.984
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]
-0.98-0.190.880.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.765
r_dihedral_angle_4_deg19.734
r_dihedral_angle_3_deg11.063
r_dihedral_angle_1_deg7.244
r_scangle_it3.817
r_scbond_it2.885
r_angle_refined_deg1.762
r_mcangle_it1.525
r_mcbond_it1.099
r_nbtor_refined0.308
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.765
r_dihedral_angle_4_deg19.734
r_dihedral_angle_3_deg11.063
r_dihedral_angle_1_deg7.244
r_scangle_it3.817
r_scbond_it2.885
r_angle_refined_deg1.762
r_mcangle_it1.525
r_mcbond_it1.099
r_nbtor_refined0.308
r_symmetry_hbond_refined0.24
r_symmetry_vdw_refined0.192
r_nbd_refined0.187
r_xyhbond_nbd_refined0.153
r_chiral_restr0.138
r_bond_refined_d0.019
r_gen_planes_refined0.008
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1798
Nucleic Acid Atoms
Solvent Atoms339
Heterogen Atoms93

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
DENZOdata reduction
HKL-2000data scaling
SCALEPACKdata scaling
PHASERphasing