X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1AIKPolyalanine-gp41 (PDB ID; 1AIK.pdb)

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP527710% PEG 6000, 50mM Na acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 4K
Crystal Properties
Matthews coefficientSolvent content
2.3747.74

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 26.366α = 90
b = 42.236β = 90
c = 43.059γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 300 mm plateosmic mirror2003-11-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RUH3R

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
11.55094.10.0719.53756125
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.51.5480.70.2215.83531

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 REPLACEMENTTHROUGHOUTPolyalanine-gp41 (PDB ID; 1AIK.pdb)1.567679710433593.670.2080.195560.195110.20537RANDOM14.817
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]
-0.59-0.441.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg49.426
r_dihedral_angle_4_deg19.785
r_dihedral_angle_3_deg10.23
r_dihedral_angle_1_deg4.025
r_angle_refined_deg0.94
r_angle_other_deg0.802
r_symmetry_vdw_other0.324
r_symmetry_vdw_refined0.261
r_nbd_refined0.202
r_symmetry_hbond_refined0.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg49.426
r_dihedral_angle_4_deg19.785
r_dihedral_angle_3_deg10.23
r_dihedral_angle_1_deg4.025
r_angle_refined_deg0.94
r_angle_other_deg0.802
r_symmetry_vdw_other0.324
r_symmetry_vdw_refined0.261
r_nbd_refined0.202
r_symmetry_hbond_refined0.18
r_nbtor_refined0.164
r_nbd_other0.153
r_xyhbond_nbd_refined0.088
r_nbtor_other0.075
r_chiral_restr0.051
r_bond_refined_d0.008
r_bond_other_d0.002
r_gen_planes_refined0.002
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
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_scbond_it
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms361
Nucleic Acid Atoms
Solvent Atoms84
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing