2VXV

Crystal structure of human IgG ABT-325 Fab Fragment


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
110.5277ABT-325 FAB FRAGMENT (20 MG/ML, 2 MICROLITERS [UL]) WAS MIXED WITH 2 UL OF A RESERVOIR SOLUTION CONSISTING OF 25 TO 30% POLYETHYLENEGLYCOL (PEG) 400, 100 MM CAPS, PH 10.5 AND SUSPENDED OVER THE RESERVOIR AT 277 K. ROD-LIKE CRYSTALS APPEARED WITHIN ONE DAY.
Crystal Properties
Matthews coefficientSolvent content
2.754.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.406α = 90
b = 74.069β = 90
c = 107.271γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMIRRORS2003-04-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 32-IDAPS32-ID

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
11.4950990.089.86.483126216
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.491.5492.30.413.14.1

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 1FNS1.4930.7178910413898.90.1550.1530.179RANDOM13.17
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]
-0.220.090.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.475
r_dihedral_angle_4_deg23.278
r_dihedral_angle_3_deg11.577
r_dihedral_angle_1_deg6.478
r_scangle_it3.533
r_scbond_it2.601
r_angle_refined_deg1.569
r_mcangle_it1.504
r_mcbond_it1.257
r_angle_other_deg0.903
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.475
r_dihedral_angle_4_deg23.278
r_dihedral_angle_3_deg11.577
r_dihedral_angle_1_deg6.478
r_scangle_it3.533
r_scbond_it2.601
r_angle_refined_deg1.569
r_mcangle_it1.504
r_mcbond_it1.257
r_angle_other_deg0.903
r_symmetry_vdw_other0.232
r_symmetry_vdw_refined0.208
r_nbd_refined0.197
r_nbd_other0.197
r_nbtor_refined0.18
r_symmetry_hbond_refined0.179
r_xyhbond_nbd_refined0.147
r_chiral_restr0.096
r_nbtor_other0.086
r_bond_refined_d0.015
r_gen_planes_refined0.007
r_gen_planes_other0.003
r_bond_other_d0.001
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_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3333
Nucleic Acid Atoms
Solvent Atoms576
Heterogen Atoms20

Software

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