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Pikromycin Thioesterase with covalent affinity label
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MNA PDB ENTRY 1MNA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.6 296 1.4 M Li2SO4, 100 mM HEPES pH 7.6, 80 mM MgCl2, 2 mM DTT, 5% DMSO, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Crystal Properties Matthews coefficient Solvent content 3.14 60.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.736 α = 90 b = 130.649 β = 90 c = 56.176 γ = 90
Symmetry Space Group P 21 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 MARMOSAIC 300 mm CCD 2005-12-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.0333 APS 23-ID-D
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 2.1 50 100 0.076 23.1 7.4 47072 47050
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.1 2.18 100 0.56 3.6 7.4
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 1MNA 2.1 83.33 47072 44658 2337 99.76 0.19536 0.19317 0.1875 0.23631 0.2275 RANDOM 39.01
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] -1.95 -0.8 2.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.353 r_dihedral_angle_3_deg 14.833 r_dihedral_angle_4_deg 13.337 r_dihedral_angle_1_deg 5.175 r_mcangle_it 3.241 r_scangle_it 3.123 r_mcbond_it 2.117 r_scbond_it 2.064 r_angle_refined_deg 1.165 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.353 r_dihedral_angle_3_deg 14.833 r_dihedral_angle_4_deg 13.337 r_dihedral_angle_1_deg 5.175 r_mcangle_it 3.241 r_scangle_it 3.123 r_mcbond_it 2.117 r_scbond_it 2.064 r_angle_refined_deg 1.165 r_nbtor_refined 0.301 r_nbd_refined 0.196 r_xyhbond_nbd_refined 0.157 r_symmetry_vdw_refined 0.155 r_symmetry_hbond_refined 0.111 r_chiral_restr 0.08 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other 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 4235 Nucleic Acid Atoms Solvent Atoms 415 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction Blu-Ice data collection SCALEPACK data scaling MOLREP phasing