2GUD

Crystal structure of a complex of griffithsin with mannose at 0.94 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
2.3848.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.74α = 90
b = 39.44β = 91
c = 57.16γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2006-02-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID0.7APS22-ID

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
10.945095.50.0643.4148669148669-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
0.940.9675

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 2GTY0.9430148669148646149895.170.13550.13550.13550.15607RANDOM8.641
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]
-0.5-0.35-0.140.62
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.7
r_dihedral_angle_4_deg17.269
r_dihedral_angle_3_deg12.48
r_sphericity_free11.393
r_dihedral_angle_1_deg7.342
r_sphericity_bonded6.485
r_angle_other_deg4.862
r_scangle_it4.273
r_scbond_it3.645
r_mcangle_it2.418
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.7
r_dihedral_angle_4_deg17.269
r_dihedral_angle_3_deg12.48
r_sphericity_free11.393
r_dihedral_angle_1_deg7.342
r_sphericity_bonded6.485
r_angle_other_deg4.862
r_scangle_it4.273
r_scbond_it3.645
r_mcangle_it2.418
r_angle_refined_deg2.154
r_mcbond_it1.945
r_rigid_bond_restr1.838
r_mcbond_other1.13
r_nbd_refined0.293
r_symmetry_vdw_refined0.271
r_symmetry_vdw_other0.263
r_nbd_other0.231
r_xyhbond_nbd_refined0.202
r_nbtor_refined0.199
r_symmetry_hbond_refined0.191
r_nbtor_other0.164
r_chiral_restr0.152
r_bond_refined_d0.024
r_gen_planes_refined0.011
r_bond_other_d0.002
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1888
Nucleic Acid Atoms
Solvent Atoms458
Heterogen Atoms105

Software

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