2NU5

Crystal structure of a complex of griffithsin cocrystallized with N-acetylglucosamine


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52931.8M magnesium sulfate, 0.1M MES, 1:10 ratio of griffithsin monomers to N-acetylglucosamine, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.0539.99

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 37.57α = 90
b = 53.41β = 90
c = 104.01γ = 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
11.5645098.80.0844.73023130231-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.5641.6292.3

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 REPLACEMENTTHROUGHOUT2GUC1.564303023128639153199.360.165070.165070.162940.20512RANDOM14.397
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]
-0.08-0.660.74
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.907
r_dihedral_angle_4_deg23.648
r_dihedral_angle_3_deg13.778
r_dihedral_angle_1_deg7.2
r_scangle_it4.636
r_scbond_it3.383
r_angle_refined_deg1.935
r_mcangle_it1.888
r_mcbond_it1.436
r_xyhbond_nbd_refined0.349
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.907
r_dihedral_angle_4_deg23.648
r_dihedral_angle_3_deg13.778
r_dihedral_angle_1_deg7.2
r_scangle_it4.636
r_scbond_it3.383
r_angle_refined_deg1.935
r_mcangle_it1.888
r_mcbond_it1.436
r_xyhbond_nbd_refined0.349
r_nbtor_refined0.316
r_nbd_refined0.276
r_symmetry_hbond_refined0.264
r_symmetry_vdw_refined0.218
r_chiral_restr0.177
r_bond_refined_d0.021
r_gen_planes_refined0.01
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 Atoms327
Heterogen Atoms105

Software

Software
Software NamePurpose
MAR345data collection
PHASERphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling