2Z2T

Crystal structure of the complex between gp41 fragment N36 and fusion inhibitor SC34EK


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4277100mM Sodium Acetate Buffer, pH4.0, 200mM Ammonium Sulphate, 14% PEG2000MME, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthew coefficientSolvent content
4.8574.62

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 105.014α = 90
b = 105.014β = 90
c = 78.308γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU JUPITER 2102007-04-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL38B11.000SPring-8BL38B1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.19099.70.1222946135.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1AIK2.119.8527843149499.760.214640.213370.23803RANDOM29.931
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]
0.010.01-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.11
r_dihedral_angle_4_deg18.85
r_dihedral_angle_3_deg15.896
r_dihedral_angle_1_deg3.788
r_scangle_it3.725
r_scbond_it2.203
r_mcangle_it1.228
r_angle_refined_deg1.015
r_mcbond_it0.806
r_nbtor_refined0.28
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.11
r_dihedral_angle_4_deg18.85
r_dihedral_angle_3_deg15.896
r_dihedral_angle_1_deg3.788
r_scangle_it3.725
r_scbond_it2.203
r_mcangle_it1.228
r_angle_refined_deg1.015
r_mcbond_it0.806
r_nbtor_refined0.28
r_nbd_refined0.183
r_symmetry_hbond_refined0.158
r_xyhbond_nbd_refined0.149
r_symmetry_vdw_refined0.125
r_chiral_restr0.075
r_bond_refined_d0.01
r_gen_planes_refined0.003
r_metal_ion_refined
r_metal_ion_other
r_sphericity_bonded
r_symmetry_vdw_other
r_nbd_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_angle_other_deg
r_mcbond_other
r_nbtor_other
r_gen_planes_other
r_bond_other_d
r_rigid_bond_restr
r_sphericity_free
r_xyhbond_nbd_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1806
Nucleic Acid Atoms
Solvent Atoms175
Heterogen Atoms29

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing