6BJZ

Crystal Structure of the Fab fragment of humanized 5c8 antibody containing the fluorescent non-canonical amino acid L-(7-hydroxycoumarin-4-yl)ethylglycine at pH 5.5


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP3.329827% PEG 3350, 0.1 M Citric Acid/Sodium Citrate pH 3.3
Crystal Properties
Matthews coefficientSolvent content
2.0540.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.813α = 90
b = 59.911β = 96.48
c = 73.459γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2016-10-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.21.00003ALS8.2.2

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
11.4572.991000.080.0860.0318.37.369300
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)
11.451.481000.7320.8020.3220.7876.1

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 REPLACEMENTTHROUGHOUT1I9R1.4572.9965883341699.890.1240.12160.1699RANDOM16.244
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]
-0.02-0.040.020.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.471
r_sphericity_free21.561
r_dihedral_angle_4_deg15.539
r_dihedral_angle_3_deg11.32
r_sphericity_bonded7.535
r_dihedral_angle_1_deg7.163
r_rigid_bond_restr2.723
r_angle_refined_deg1.723
r_angle_other_deg1.003
r_chiral_restr0.113
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.471
r_sphericity_free21.561
r_dihedral_angle_4_deg15.539
r_dihedral_angle_3_deg11.32
r_sphericity_bonded7.535
r_dihedral_angle_1_deg7.163
r_rigid_bond_restr2.723
r_angle_refined_deg1.723
r_angle_other_deg1.003
r_chiral_restr0.113
r_bond_refined_d0.014
r_gen_planes_refined0.004
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3303
Nucleic Acid Atoms
Solvent Atoms525
Heterogen Atoms

Software

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