4NZU | pdb_00004nzu

Crystal structure of the primary monoclonal antibody 13PL Fab' from a multiple myeloma patient


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1HILPDB ENTRY 1HIL

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP42950.1 M citric acid, pH 4.0, 1.0 M lithium chloride, 23% PEG6000, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.2645.45

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.179α = 90
b = 80.403β = 90
c = 102.607γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2012-02-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL11-10.97945SSRLBL11-1

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
11.263.28795.10.0527.46.2126314-3
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)
11.21.2273.70.621.23.6

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1HIL1.263.287119898635595.130.137210.135850.150.163330.17RANDOM13.771
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]
-0.650.090.56
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.26
r_sphericity_free24.898
r_dihedral_angle_4_deg24.411
r_dihedral_angle_3_deg9.998
r_sphericity_bonded9.347
r_dihedral_angle_1_deg6.656
r_rigid_bond_restr1.555
r_angle_refined_deg1.34
r_angle_other_deg0.829
r_chiral_restr0.076
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.26
r_sphericity_free24.898
r_dihedral_angle_4_deg24.411
r_dihedral_angle_3_deg9.998
r_sphericity_bonded9.347
r_dihedral_angle_1_deg6.656
r_rigid_bond_restr1.555
r_angle_refined_deg1.34
r_angle_other_deg0.829
r_chiral_restr0.076
r_bond_refined_d0.008
r_gen_planes_refined0.006
r_bond_other_d0.002
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_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3270
Nucleic Acid Atoms
Solvent Atoms586
Heterogen Atoms28

Software

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