3CFJ | pdb_00003cfj

Crystal structure of catalytic elimination antibody 34E4, orthorhombic crystal form


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1Y0LPDB ENTRY 1Y0L

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
14.630% MPEG 2000, 0.2M (NH4)2SO4, 0.1M ACETATE, PH 4.6, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K, pH 4.60
Crystal Properties
Matthews coefficientSolvent content
2.5952.48

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.137α = 90
b = 114.471β = 90
c = 212.131γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210MONOCHROMATOR2005-01-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.1ALS8.2.1

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
12.65099.70.10811.94.16355151.4
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)
12.62.6999.90.62824.1

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1Y0L2.648.3458339309499.80.2020.1990.20.2530.25RANDOM38.44
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]
-0.551.79-1.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.31
r_dihedral_angle_4_deg18.933
r_dihedral_angle_3_deg16.889
r_dihedral_angle_1_deg6.311
r_scangle_it3.111
r_scbond_it2.093
r_angle_refined_deg1.42
r_mcangle_it1.069
r_mcbond_it0.937
r_nbtor_refined0.306
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.31
r_dihedral_angle_4_deg18.933
r_dihedral_angle_3_deg16.889
r_dihedral_angle_1_deg6.311
r_scangle_it3.111
r_scbond_it2.093
r_angle_refined_deg1.42
r_mcangle_it1.069
r_mcbond_it0.937
r_nbtor_refined0.306
r_symmetry_vdw_refined0.258
r_nbd_refined0.215
r_symmetry_hbond_refined0.206
r_xyhbond_nbd_refined0.148
r_chiral_restr0.093
r_bond_refined_d0.013
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms13377
Nucleic Acid Atoms
Solvent Atoms518
Heterogen Atoms33

Software

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