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Crystal structure of human apurinic/apyrimidinic endonuclease 1 with essential Mg2+ cofactor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BIX PDB ENTRY 1BIX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 295 0.1 M MES pH 6.5, 30% (v/v) PEG 300, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 3.08 60.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 165.795 α = 90 b = 90.94 β = 123.22 c = 94.03 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 100 CCD ADSC QUANTUM 315r 2012-01-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL7-1 1.03325 SSRL BL7-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.92 69.35 85.4 0.1 3.6 2.5 75632 75632 -3
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 1.92 1.96 84.4 0.63 0.7 2.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 1BIX 1.92 48 75632 71263 3746 84.38 0.2185 0.21734 0.2236 0.24052 0.2361 RANDOM 34.649
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] 0.58 0.91 -0.25 -0.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.472 r_dihedral_angle_4_deg 18.7 r_dihedral_angle_3_deg 13.49 r_dihedral_angle_1_deg 6.333 r_angle_other_deg 3.37 r_long_range_B_refined 2.846 r_long_range_B_other 2.841 r_mcangle_it 1.295 r_mcangle_other 1.294 r_angle_refined_deg 1.243
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.472 r_dihedral_angle_4_deg 18.7 r_dihedral_angle_3_deg 13.49 r_dihedral_angle_1_deg 6.333 r_angle_other_deg 3.37 r_long_range_B_refined 2.846 r_long_range_B_other 2.841 r_mcangle_it 1.295 r_mcangle_other 1.294 r_angle_refined_deg 1.243 r_scangle_other 1.21 r_mcbond_it 0.783 r_mcbond_other 0.783 r_scbond_it 0.73 r_scbond_other 0.73 r_chiral_restr 0.071 r_bond_refined_d 0.008 r_gen_planes_other 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6331 Nucleic Acid Atoms Solvent Atoms 120 Heterogen Atoms 3
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement MOSFLM data reduction Aimless data scaling