6W4W

Crystal Structure of the Fab fragment of humanized 5c8 antibody


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1I9R 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP27333% PEG 3350, 0.1 M Citric Acid/Sodium Citrate pH 4.0
Crystal Properties
Matthews coefficientSolvent content
2.0941.04

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.894α = 90
b = 60.305β = 96.27
c = 73.456γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2016-04-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.97934APS19-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
11.7750.1698.10.0520.0570.02211.16.338013
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.771.894.40.3240.3560.1430.9365.6

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1i9r1.7750.1636102185398.240.1710.16930.2042RANDOM24.955
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]
-0.090.050.21-0.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.406
r_dihedral_angle_4_deg22.575
r_dihedral_angle_3_deg12.34
r_dihedral_angle_1_deg8.671
r_angle_refined_deg1.758
r_angle_other_deg0.953
r_chiral_restr0.1
r_bond_refined_d0.015
r_gen_planes_refined0.003
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.406
r_dihedral_angle_4_deg22.575
r_dihedral_angle_3_deg12.34
r_dihedral_angle_1_deg8.671
r_angle_refined_deg1.758
r_angle_other_deg0.953
r_chiral_restr0.1
r_bond_refined_d0.015
r_gen_planes_refined0.003
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3205
Nucleic Acid Atoms
Solvent Atoms271
Heterogen Atoms

Software

Software
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction