3GIZ

Crystal structure of the Fab fragment of anti-CD20 antibody Ofatumumab


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1U6APDB ENTRY 1U6A

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.32770.2 M zinc acetate, 20% PEG3350, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.7555.21

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 136.33α = 90
b = 55.944β = 122.17
c = 79.78γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++2008-06-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.22099.40.0830.08375.1262082605135
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.22.2899.40.3250.3252.14.82618

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 1U6A2.2202589924611128899.420.197520.197520.194770.24957RANDOM28.506
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]
-0.24-0.171.2-1.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.65
r_dihedral_angle_4_deg24.796
r_dihedral_angle_3_deg15.682
r_dihedral_angle_1_deg6.977
r_sphericity_free3.956
r_scangle_it2.318
r_scbond_it1.563
r_angle_refined_deg1.375
r_sphericity_bonded1.337
r_mcangle_it1.175
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.65
r_dihedral_angle_4_deg24.796
r_dihedral_angle_3_deg15.682
r_dihedral_angle_1_deg6.977
r_sphericity_free3.956
r_scangle_it2.318
r_scbond_it1.563
r_angle_refined_deg1.375
r_sphericity_bonded1.337
r_mcangle_it1.175
r_rigid_bond_restr1.144
r_mcbond_it0.696
r_symmetry_vdw_refined0.315
r_nbtor_refined0.3
r_symmetry_metal_ion_refined0.294
r_nbd_refined0.196
r_xyhbond_nbd_refined0.138
r_symmetry_hbond_refined0.095
r_chiral_restr0.093
r_metal_ion_refined0.053
r_bond_refined_d0.011
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3261
Nucleic Acid Atoms
Solvent Atoms221
Heterogen Atoms3

Software

Software
Software NamePurpose
CrystalCleardata collection
PHASERphasing
REFMACrefinement
CrystalCleardata reduction
CrystalCleardata scaling