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A Second Divalent Metal Ion in the Active Site of a New Crystal Form of Human Apurinic/Apyridinimic Endonuclease, Ape1, and its Implications for the Catalytic Mechanism
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other TO BE PUBLISHED
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.5 0.1M NAOAC PH 4.6, 25% PEG 4K, 1 MM PB(II)OAC, 10-12 MG/ML PROTEIN.
Crystal Properties Matthews coefficient Solvent content 2.7 54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.39 α = 90 b = 44.85 β = 124.54 c = 78.14 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 CCD ADSC CCD DUAL CRYSTAL MIRROR 1999-03-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL1-5 SSRL BL1-5
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.95 25 99.4 0.082 6.6 3.3 34905 29.68
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2.01 99.2 0.47 1.5 3.2
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT TO BE PUBLISHED 1.95 25 26771 2699 92.2 0.205 0.2044 0.255 RANDOM 37.4
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]
RMS Deviations Key Refinement Restraint Deviation p_transverse_tor 31.7 p_staggered_tor 18.1 p_planar_tor 8.4 p_scangle_it 3.4 p_mcangle_it 2.7 p_scbond_it 2.2 p_mcbond_it 1.8 p_multtor_nbd 0.261 p_singtor_nbd 0.185 p_chiral_restr 0.15
RMS Deviations Key Refinement Restraint Deviation p_transverse_tor 31.7 p_staggered_tor 18.1 p_planar_tor 8.4 p_scangle_it 3.4 p_mcangle_it 2.7 p_scbond_it 2.2 p_mcbond_it 1.8 p_multtor_nbd 0.261 p_singtor_nbd 0.185 p_chiral_restr 0.15 p_xyhbond_nbd 0.125 p_planar_d 0.069 p_angle_d 0.038 p_plane_restr 0.03 p_bond_d 0.016 p_angle_deg p_hb_or_metal_coord p_xhyhbond_nbd p_orthonormal_tor p_special_tor
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2070 Nucleic Acid Atoms Solvent Atoms 288 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling EPMR phasing