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Crystal structure of TM1086
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DCL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 5.6 295 60% Tacsimate, 0.1M Na citrate, pH 5.6, VAPOR DIFFUSION, temperature 295K
Crystal Properties Matthews coefficient Solvent content 3.67 66.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 289.839 α = 90 b = 299.521 β = 90 c = 316.013 γ = 90
Symmetry Space Group I 2 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 MARMOSAIC 300 mm CCD MIRRORS 2006-07-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 0.9793 APS 23-ID-B
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 2.38 50 100 0.113 0.113 19.7 7.2 537068 537068 -3 35
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) 2.4 2.44 100 0.55 0.55 3.4 6.6 26709
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 (All) 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 3DCL 2.38 50 509826 509826 26930 99.12 0.15338 0.15338 0.1514 0.1544 0.1913 0.1925 RANDOM 25.764
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] -0.16 0.37 -0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.46 r_dihedral_angle_4_deg 20.194 r_dihedral_angle_3_deg 13.514 r_dihedral_angle_1_deg 6.679 r_scangle_it 5.744 r_angle_other_deg 4.293 r_scbond_it 3.256 r_mcangle_it 1.907 r_angle_refined_deg 1.694 r_mcbond_it 0.928
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.46 r_dihedral_angle_4_deg 20.194 r_dihedral_angle_3_deg 13.514 r_dihedral_angle_1_deg 6.679 r_scangle_it 5.744 r_angle_other_deg 4.293 r_scbond_it 3.256 r_mcangle_it 1.907 r_angle_refined_deg 1.694 r_mcbond_it 0.928 r_chiral_restr 0.098 r_bond_refined_d 0.02 r_gen_planes_refined 0.007 r_gen_planes_other 0.007 r_bond_other_d 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_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 63060 Nucleic Acid Atoms Solvent Atoms 5054 Heterogen Atoms 86
Software Software Software Name Purpose Blu-Ice data collection MOLREP phasing REFMAC refinement Coot model building HKL-2000 data reduction HKL-2000 data scaling