3W9E

Structure of Human Monoclonal Antibody E317 Fab Complex with HSV-2 gD


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION8.229530%(v/v) PEG 550MME, 0.1M Na HEPES, pH 8.2, VAPOR DIFFUSION, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.7555.28

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.029α = 90
b = 91.087β = 90
c = 141.537γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298CCDRAYONIX MX-2252012-10-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL41XU0.9000SPring-8BL41XU

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
12.33098.50.06126.26.438408378321

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 REPLACEMENTTHROUGHOUT1L2G, 3W9D2.329.7837832199698.50.206130.206130.203480.25544RANDOM52.342
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]
5.26-2.52-2.75
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.626
r_dihedral_angle_4_deg18.618
r_dihedral_angle_3_deg15.759
r_dihedral_angle_1_deg6.358
r_angle_refined_deg1.354
r_angle_other_deg0.875
r_chiral_restr0.127
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.626
r_dihedral_angle_4_deg18.618
r_dihedral_angle_3_deg15.759
r_dihedral_angle_1_deg6.358
r_angle_refined_deg1.354
r_angle_other_deg0.875
r_chiral_restr0.127
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
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 Atoms5039
Nucleic Acid Atoms
Solvent Atoms252
Heterogen Atoms64

Software

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