1YED

STRUCTURE OF A CATALYTIC ANTIBODY IGG2A FAB FRAGMENT (D2.4)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1YECPDB ENTRY 1YEC FOR THE VARIABLE DOMAINS AND PDB ENTRY 1DFB FOR THE CONSTANT DOMAINS
experimental modelPDB 1DFBPDB ENTRY 1YEC FOR THE VARIABLE DOMAINS AND PDB ENTRY 1DFB FOR THE CONSTANT DOMAINS

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17pH 7.0
Crystal Properties
Matthews coefficientSolvent content
2.9958.88

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 99.25α = 90
b = 104.79β = 90
c = 223.75γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298IMAGE PLATEMARRESEARCH1995-09-12M
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONLURE BEAMLINE D41ALURED41A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
13.12087.60.0712.7187221

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTPDB ENTRY 1YEC FOR THE VARIABLE DOMAINS AND PDB ENTRY 1DFB FOR THE CONSTANT DOMAINS3.172509370.2150.2150.26
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]
RMS Deviations
KeyRefinement Restraint Deviation
x_dihedral_angle_d28.02
x_angle_deg1.647
x_improper_angle_d1.408
x_bond_d0.008
x_bond_d_na
x_bond_d_prot
x_angle_d
x_angle_d_na
x_angle_d_prot
x_angle_deg_na
RMS Deviations
KeyRefinement Restraint Deviation
x_dihedral_angle_d28.02
x_angle_deg1.647
x_improper_angle_d1.408
x_bond_d0.008
x_bond_d_na
x_bond_d_prot
x_angle_d
x_angle_d_na
x_angle_d_prot
x_angle_deg_na
x_angle_deg_prot
x_dihedral_angle_d_na
x_dihedral_angle_d_prot
x_improper_angle_d_na
x_improper_angle_d_prot
x_mcbond_it
x_mcangle_it
x_scbond_it
x_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6834
Nucleic Acid Atoms
Solvent Atoms4
Heterogen Atoms48

Software

Software
Software NamePurpose
MOSFLMdata reduction
CCP4data reduction
X-PLORmodel building
X-PLORrefinement
CCP4data scaling
X-PLORphasing