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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 1L2E PDB ENTRY 1L2E, 1RJL experimental model PDB 1RJL PDB ENTRY 1L2E, 1RJL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.2 293 14% MPEG 550, 100mM HEPES, pH7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.05 59.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.36 α = 90 b = 87.36 β = 90 c = 236.332 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 2006-04-21 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 2.8 78.81 100 0.159 0.168 14.5 9.5 23506
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) 2.8 2.95 100 0.498 0.525 3.7 9.7 3342
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 1L2E, 1RJL 2.83 78.81 21615 1168 100 0.20652 0.2032 0.2095 0.27033 0.2683 RANDOM 38.776
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] 0.3 0.3 -0.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.157 r_dihedral_angle_3_deg 19.424 r_dihedral_angle_4_deg 17.805 r_dihedral_angle_1_deg 8.083 r_scangle_it 3.072 r_scbond_it 2.043 r_angle_refined_deg 1.874 r_mcangle_it 1.433 r_mcbond_it 1.399 r_angle_other_deg 0.973
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.157 r_dihedral_angle_3_deg 19.424 r_dihedral_angle_4_deg 17.805 r_dihedral_angle_1_deg 8.083 r_scangle_it 3.072 r_scbond_it 2.043 r_angle_refined_deg 1.874 r_mcangle_it 1.433 r_mcbond_it 1.399 r_angle_other_deg 0.973 r_symmetry_vdw_other 0.256 r_nbd_refined 0.227 r_nbd_other 0.221 r_symmetry_hbond_refined 0.216 r_nbtor_refined 0.191 r_xyhbond_nbd_refined 0.167 r_symmetry_vdw_refined 0.15 r_mcbond_other 0.109 r_chiral_restr 0.103 r_nbtor_other 0.097 r_xyhbond_nbd_other 0.046 r_bond_refined_d 0.018 r_gen_planes_refined 0.006 r_bond_other_d 0.005 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5188 Nucleic Acid Atoms Solvent Atoms 66 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection MOSFLM data reduction PROCESS data scaling XFIT data reduction