2ZCL | pdb_00002zcl

Crystal structure of human prostate specific antigen complexed with an activating antibody


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2ZCHPDB entry 2ZCH

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.2293crystals grown in 14% MPEG550, 100mM HEPES (pH7.2), then soaked in 33% PEG400, 100mM MES (pH5.5), 10mM ZnCl2, 0.28mg/ml Mu-KGISSQY-AFC, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.160.27

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 87.978α = 90
b = 87.978β = 90
c = 238.063γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray200CCDMARMOSAIC 225 mm CCD2006-09-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-20.873ESRFID23-2

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
13.2588.0499.90.1440.15414.9815532
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)
13.253.4399.40.4670.4984.97.32175

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 2ZCH3.2582.481468777099.810.203790.201390.20.250980.25RANDOM65.319
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]
0.360.36-0.72
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.775
r_dihedral_angle_3_deg22.186
r_dihedral_angle_4_deg20.201
r_dihedral_angle_1_deg8.147
r_angle_refined_deg1.742
r_mcangle_it1.541
r_mcbond_it1.197
r_scangle_it1.11
r_angle_other_deg0.875
r_scbond_it0.676
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5219
Nucleic Acid Atoms
Solvent Atoms12
Heterogen Atoms28

Software

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