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Crystal Structure of the N-terminal Catalytic Domain of TP901-1 Integrase
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 294 PEG8000, Mg(OAc)2, pH 6.0, vapor diffusion, hanging drop, temperature 294K
Crystal Properties Matthews coefficient Solvent content 3.12 60.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.229 α = 90 b = 67.229 β = 90 c = 174.565 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 100 CCD ADSC QUANTUM 4 2007-07-08 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD ADSC QUANTUM 315 2007-07-08 M MAD 3 1 x-ray 100 CCD ADSC QUANTUM 315 2007-07-09 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.1 1.0093 ALS 8.2.1 2 SYNCHROTRON ALS BEAMLINE 8.2.1 0.9200, 0.9203, 0.9099 ALS 8.2.1 3 SYNCHROTRON ALS BEAMLINE 8.2.1 1.0722, 1.0726, 1.0540 ALS 8.2.1
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 1,2,3 2.1 50 96.4 0.056 15.8 8.1 23563
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) 1,2,3 2.1 2.18 77.8 0.44 5.1 1863
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MAD THROUGHOUT 2.1 44 23494 1195 96.44 0.201 0.198 0.1994 0.263 0.2549 RANDOM 64.09
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] 1.93 1.93 -3.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.652 r_dihedral_angle_4_deg 19.979 r_dihedral_angle_3_deg 16.294 r_dihedral_angle_1_deg 4.846 r_mcangle_it 1.475 r_scangle_it 1.436 r_angle_refined_deg 1.212 r_scbond_it 0.949 r_mcbond_it 0.912 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.652 r_dihedral_angle_4_deg 19.979 r_dihedral_angle_3_deg 16.294 r_dihedral_angle_1_deg 4.846 r_mcangle_it 1.475 r_scangle_it 1.436 r_angle_refined_deg 1.212 r_scbond_it 0.949 r_mcbond_it 0.912 r_nbtor_refined 0.306 r_nbd_refined 0.211 r_symmetry_vdw_refined 0.186 r_xyhbond_nbd_refined 0.175 r_symmetry_hbond_refined 0.135 r_chiral_restr 0.09 r_bond_refined_d 0.011 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2132 Nucleic Acid Atoms Solvent Atoms 200 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling SOLVE phasing RESOLVE phasing REFMAC refinement PDB_EXTRACT data extraction