2NUO

Crystal structure of a complex of griffithsin with glucose


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2GUCPDB ENTRY 2guc

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52931.2M magnesium sulfate, 0.1M MES, 1:10 ratio of griffithsin monomers to glucose, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.0540.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 37.49α = 90
b = 53.67β = 90
c = 103.83γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2006-06-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1.0APS22-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
11.55089.60.083082030820-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.51.5597.3

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 2guc1.5303082029215155989.210.15710.15710.154580.20347RANDOM8.775
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]
-0.02-0.280.29
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.772
r_dihedral_angle_4_deg20.979
r_dihedral_angle_3_deg15.598
r_dihedral_angle_1_deg7.316
r_scangle_it4.427
r_angle_other_deg3.929
r_scbond_it3.44
r_angle_refined_deg2.096
r_mcangle_it1.949
r_mcbond_it1.646
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.772
r_dihedral_angle_4_deg20.979
r_dihedral_angle_3_deg15.598
r_dihedral_angle_1_deg7.316
r_scangle_it4.427
r_angle_other_deg3.929
r_scbond_it3.44
r_angle_refined_deg2.096
r_mcangle_it1.949
r_mcbond_it1.646
r_mcbond_other0.357
r_symmetry_vdw_other0.356
r_symmetry_hbond_refined0.33
r_nbd_refined0.238
r_chiral_restr0.23
r_nbd_other0.213
r_xyhbond_nbd_refined0.194
r_nbtor_refined0.182
r_symmetry_vdw_refined0.167
r_nbtor_other0.103
r_bond_refined_d0.021
r_bond_other_d0.01
r_gen_planes_refined0.01
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
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 Atoms288
Heterogen Atoms81

Software

Software
Software NamePurpose
REFMACrefinement
MAR345data collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing