2ZCK

Crystal structure of a ternary complex between PSA, a substrat-acyl intermediate and an activating antibody


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.2293crystal grown in 14% MPEG550, 100mM HEPES (pH7.2), then soaked in PEG400, 100mM Tris-HCl (pH7.3), 10mM ZnCl2, 0.28 mg/ml Mu-KGISSQY-AFC, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.9858.74

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 86.765α = 90
b = 86.765β = 90
c = 238.18γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray200CCDADSC QUANTUM 42006-06-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-20.933ESRFID14-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
13.170.1999.20.1150.12712.85.517100
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.13.2798.40.5190.5832.34.42397

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 REPLACEMENTTHROUGHOUTpdb entry 2ZCH3.170.191621787098.730.22340.220640.27522RANDOM62.772
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]
1.111.11-2.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.733
r_dihedral_angle_3_deg18.849
r_dihedral_angle_4_deg16.009
r_dihedral_angle_1_deg8.335
r_scangle_it2.342
r_angle_refined_deg1.733
r_scbond_it1.578
r_mcangle_it1.149
r_mcbond_it1.136
r_angle_other_deg0.974
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.733
r_dihedral_angle_3_deg18.849
r_dihedral_angle_4_deg16.009
r_dihedral_angle_1_deg8.335
r_scangle_it2.342
r_angle_refined_deg1.733
r_scbond_it1.578
r_mcangle_it1.149
r_mcbond_it1.136
r_angle_other_deg0.974
r_chiral_restr0.241
r_nbd_refined0.211
r_nbd_other0.201
r_nbtor_refined0.183
r_symmetry_vdw_refined0.178
r_symmetry_hbond_refined0.173
r_xyhbond_nbd_refined0.166
r_symmetry_vdw_other0.161
r_nbtor_other0.091
r_mcbond_other0.064
r_bond_refined_d0.015
r_bond_other_d0.007
r_gen_planes_refined0.005
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5273
Nucleic Acid Atoms
Solvent Atoms31
Heterogen Atoms25

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data collection
MOSFLMdata reduction
PROCESSdata scaling
XFITdata reduction