6W5A

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 9.7


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6BJZ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP27330% PEG 3350, 0.1 M Citric Acid/Sodium Citrate pH 3.8
Crystal Properties
Matthews coefficientSolvent content
2.0840.88

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.861α = 90
b = 60.182β = 98.94
c = 73.258γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2016-11-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.91976APS19-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
11.7572.37990.1530.1750.0825.34.239519
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)
11.751.7899.50.6940.8040.40.6623.7

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 REPLACEMENTTHROUGHOUT6bjz1.7572.3737564195598.770.19490.19250.2407RANDOM29.291
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]
0.790.65-0.01-0.94
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.393
r_dihedral_angle_4_deg17.195
r_dihedral_angle_3_deg12.152
r_dihedral_angle_1_deg7.444
r_angle_refined_deg1.723
r_angle_other_deg0.973
r_chiral_restr0.101
r_bond_refined_d0.014
r_gen_planes_refined0.003
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.393
r_dihedral_angle_4_deg17.195
r_dihedral_angle_3_deg12.152
r_dihedral_angle_1_deg7.444
r_angle_refined_deg1.723
r_angle_other_deg0.973
r_chiral_restr0.101
r_bond_refined_d0.014
r_gen_planes_refined0.003
r_bond_other_d0.002
r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3210
Nucleic Acid Atoms
Solvent Atoms271
Heterogen Atoms

Software

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