2B0S

Crystal structure analysis of anti-HIV-1 V3 Fab 2219 in complex with MN peptide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7FABpdb entry 7FAB

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29840% PEG 400, 0.2M potassium acetate, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K
Crystal Properties
Matthews coefficientSolvent content
2.551

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.471α = 90
b = 60.471β = 90
c = 275.194γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152002-06-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-21.033SSRLBL9-2

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
12.369.0199.80.086225.32383523835-330.8
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)
12.32.341000.5253.55.51162

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 7FAB2.369.012262422624119599.810.219260.219260.216850.26665RANDOM31.648
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]
0.950.95-1.89
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.716
r_dihedral_angle_3_deg13.882
r_dihedral_angle_4_deg12.049
r_dihedral_angle_1_deg7.231
r_scangle_it2.133
r_scbond_it1.494
r_angle_refined_deg1.458
r_mcangle_it0.937
r_angle_other_deg0.92
r_mcbond_it0.751
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.716
r_dihedral_angle_3_deg13.882
r_dihedral_angle_4_deg12.049
r_dihedral_angle_1_deg7.231
r_scangle_it2.133
r_scbond_it1.494
r_angle_refined_deg1.458
r_mcangle_it0.937
r_angle_other_deg0.92
r_mcbond_it0.751
r_symmetry_vdw_other0.241
r_nbd_refined0.206
r_nbd_other0.189
r_nbtor_refined0.177
r_symmetry_hbond_refined0.169
r_xyhbond_nbd_refined0.162
r_symmetry_vdw_refined0.144
r_chiral_restr0.13
r_mcbond_other0.127
r_nbtor_other0.085
r_bond_refined_d0.013
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3449
Nucleic Acid Atoms
Solvent Atoms191
Heterogen Atoms20

Software

Software
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
DENZOdata reduction