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Crystal structure of kirola (Act d 11) from crystal soaked with 2-aminopurine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4IGV PDB ENTRY 4IGV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293 0.15 M citric acid, 0.3 M magnesium chloride, 0.01 M calcium chloride, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.43 49.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.592 α = 90 b = 71.592 β = 90 c = 114.446 γ = 120
Symmetry Space Group P 63 2 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 315 2010-06-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9793 APS 19-ID
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 50 99.5 0.095 0.095 44.6 10.8 12396 12396 -3 28
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 2 2.03 100 0.622 0.622 5.8 11.2 590
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 FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 4IGV 2 50 11691 11691 594 99.55 0.19943 0.1973 0.2001 0.24423 0.2514 RANDOM 37.928
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] 2.86 1.43 2.86 -4.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.862 r_dihedral_angle_4_deg 15.636 r_dihedral_angle_3_deg 13.788 r_dihedral_angle_1_deg 5.667 r_angle_refined_deg 1.724 r_angle_other_deg 1.053 r_chiral_restr 0.12 r_bond_refined_d 0.016 r_bond_other_d 0.01 r_gen_planes_refined 0.007
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.862 r_dihedral_angle_4_deg 15.636 r_dihedral_angle_3_deg 13.788 r_dihedral_angle_1_deg 5.667 r_angle_refined_deg 1.724 r_angle_other_deg 1.053 r_chiral_restr 0.12 r_bond_refined_d 0.016 r_bond_other_d 0.01 r_gen_planes_refined 0.007 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_scbond_it r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1187 Nucleic Acid Atoms Solvent Atoms 98 Heterogen Atoms 11
Software Software Software Name Purpose HKL-3000 data collection HKL-3000 phasing MOLREP phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling