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New crystal form of transcriptional regulator tm1030 from Thermotoga maritima
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZKG PDB entry 1zkg
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 293 0.05M Na citrate, 30% w/v PEG 2K MME, 0.1M KSCN, 0.01M NH4 sulfate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.13 42.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.566 α = 90 b = 52.286 β = 92.9 c = 49.665 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 315 mirrors 2005-06-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97940 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 1.83 50 98.3 0.128 0.146 28.8 4.6 17541 17541 -3
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) 1.83 1.9 100 0.437 0.463 4.3 4.6 1788
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 PDB entry 1zkg 1.83 19.87 16860 16860 903 98.07 0.22159 0.22159 0.21893 0.2291 0.26915 0.283 RANDOM 28.435
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] 3.46 -1.26 -2.58 -1.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.096 r_dihedral_angle_4_deg 18.041 r_dihedral_angle_3_deg 13.675 r_scangle_it 4.699 r_dihedral_angle_1_deg 4.535 r_scbond_it 3.282 r_mcangle_it 1.663 r_angle_refined_deg 1.504 r_mcbond_it 1.381 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.096 r_dihedral_angle_4_deg 18.041 r_dihedral_angle_3_deg 13.675 r_scangle_it 4.699 r_dihedral_angle_1_deg 4.535 r_scbond_it 3.282 r_mcangle_it 1.663 r_angle_refined_deg 1.504 r_mcbond_it 1.381 r_nbtor_refined 0.309 r_nbd_refined 0.22 r_symmetry_hbond_refined 0.196 r_xyhbond_nbd_refined 0.188 r_symmetry_vdw_refined 0.185 r_chiral_restr 0.11 r_bond_refined_d 0.018 r_gen_planes_refined 0.007 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 1596 Nucleic Acid Atoms Solvent Atoms 126 Heterogen Atoms 19
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing