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Crystal structure of human prostate specific antigen complexed with an activating antibody
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ZCH PDB entry 2ZCH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.2 293 crystals 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 coefficient Solvent content 3.1 60.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.978 α = 90 b = 87.978 β = 90 c = 238.063 γ = 90
Symmetry Space Group P 41 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 200 CCD MARMOSAIC 225 mm CCD 2006-09-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.873 ESRF ID23-2
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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 3.25 88.04 99.9 0.144 0.154 14.9 8 15532
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) Redundancy Number Unique Reflections (All) 1 3.25 3.43 99.4 0.467 0.498 4.9 7.3 2175
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (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 Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 2ZCH 3.25 82.48 14687 770 99.81 0.20379 0.20139 0.2019 0.25098 0.2518 RANDOM 65.319
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] 0.36 0.36 -0.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.775 r_dihedral_angle_3_deg 22.186 r_dihedral_angle_4_deg 20.201 r_dihedral_angle_1_deg 8.147 r_angle_refined_deg 1.742 r_mcangle_it 1.541 r_mcbond_it 1.197 r_scangle_it 1.11 r_angle_other_deg 0.875 r_scbond_it 0.676
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.775 r_dihedral_angle_3_deg 22.186 r_dihedral_angle_4_deg 20.201 r_dihedral_angle_1_deg 8.147 r_angle_refined_deg 1.742 r_mcangle_it 1.541 r_mcbond_it 1.197 r_scangle_it 1.11 r_angle_other_deg 0.875 r_scbond_it 0.676 r_nbd_refined 0.221 r_nbd_other 0.213 r_symmetry_vdw_other 0.209 r_symmetry_vdw_refined 0.202 r_nbtor_refined 0.197 r_xyhbond_nbd_refined 0.153 r_mcbond_other 0.135 r_symmetry_hbond_refined 0.119 r_nbtor_other 0.099 r_xyhbond_nbd_other 0.085 r_chiral_restr 0.084 r_bond_refined_d 0.017 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 Atoms Number Protein Atoms 5219 Nucleic Acid Atoms Solvent Atoms 12 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection MOSFLM data reduction PROCESS data scaling XFIT data reduction