2GUE

Crystal structure of a complex of griffithsin with N-acetylglucosamine


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP42930.2 M ammonium sulfate, 30% PEG 4000; crystal soaked in a reservoir solution supplemented with 50mM N-acetylglucosamine, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.0941.18

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 33.83α = 90
b = 65.45β = 90
c = 96.18γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plate2005-12-08MSINGLE 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
12.025092.80.0851360613606-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.022.0956

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 2GTY2.0230136061356367093.20.19930.19930.19930.274RANDOM29.875
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]
1.57-0.59-0.99
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.123
r_dihedral_angle_4_deg17.033
r_dihedral_angle_3_deg16.085
r_dihedral_angle_1_deg8.227
r_scangle_it3.928
r_scbond_it2.94
r_angle_refined_deg1.969
r_mcangle_it1.796
r_mcbond_it1.098
r_nbtor_refined0.308
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.123
r_dihedral_angle_4_deg17.033
r_dihedral_angle_3_deg16.085
r_dihedral_angle_1_deg8.227
r_scangle_it3.928
r_scbond_it2.94
r_angle_refined_deg1.969
r_mcangle_it1.796
r_mcbond_it1.098
r_nbtor_refined0.308
r_xyhbond_nbd_refined0.287
r_symmetry_vdw_refined0.25
r_nbd_refined0.246
r_symmetry_hbond_refined0.236
r_chiral_restr0.121
r_bond_refined_d0.02
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 Atoms124
Heterogen Atoms124

Software

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