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Crystal structure of transcriptional regulator (tm1030) at 1.75A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Z77
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 3%w/v Dextrose, 30%w/v PEG 2K MME, 0.1 M KSCN, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.1 41.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.765 α = 90 b = 66.012 β = 90 c = 55.623 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 ADSC QUANTUM 315 mirrors 2006-06-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 1.27819 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 1.746 33.83 99.3 0.062 0.061 45.9 7.3 21489 21339 -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) 1.746 1.81 98 0.397 0.365 2.9 5.8 2043
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 isomorphous replacement THROUGHOUT 1Z77 1.746 33.83 20076 20076 1091 98.6 0.21136 0.21136 0.20916 0.2239 0.25102 0.2497 RANDOM 32.019
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] -0.64 -0.17 0.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.256 r_dihedral_angle_4_deg 21.717 r_dihedral_angle_3_deg 13.814 r_dihedral_angle_1_deg 4.425 r_scangle_it 4.379 r_scbond_it 3.355 r_mcangle_it 1.551 r_angle_refined_deg 1.493 r_mcbond_it 1.313 r_nbtor_refined 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.256 r_dihedral_angle_4_deg 21.717 r_dihedral_angle_3_deg 13.814 r_dihedral_angle_1_deg 4.425 r_scangle_it 4.379 r_scbond_it 3.355 r_mcangle_it 1.551 r_angle_refined_deg 1.493 r_mcbond_it 1.313 r_nbtor_refined 0.311 r_symmetry_vdw_refined 0.28 r_nbd_refined 0.21 r_symmetry_hbond_refined 0.16 r_xyhbond_nbd_refined 0.14 r_chiral_restr 0.098 r_bond_refined_d 0.022 r_gen_planes_refined 0.006 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 1657 Nucleic Acid Atoms Solvent Atoms 151 Heterogen Atoms 4
Software Software Software Name Purpose HKL-2000 data collection REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling CCP4 phasing Coot model building REFMAC phasing