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Crystal structure of THI-4 protein from Bacillus subtilis
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 295 2M Hexanediol, 0.2M CaCl2, 0.1M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.22 44.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.38 α = 90 b = 58.38 β = 90 c = 296.24 γ = 90
Symmetry Space Group P 41 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 77 CCD MARRESEARCH 2003-10-01 M SAD 2 1 x-ray 77 CCD MARRESEARCH 2003-12-05 M SAD 1,2 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 5ID-B 0.979 APS 5ID-B 2 SYNCHROTRON APS BEAMLINE 5ID-B 0.979 APS 5ID-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 2.4 30 99.7 0.045 0.039 7 21219 21219
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 2.4 2.45 99.7 0.117 0.089 7.5 3.8 1239
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 2.4 30 21219 20042 1084 99.66 0.21237 0.21237 0.21017 0.25689 0.2829 RANDOM 41.918
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] 2.1 2.1 -4.19
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 11.122 r_scbond_it 8.544 r_mcangle_it 6.359 r_mcbond_it 4.389 r_dihedral_angle_1_deg 4.116 r_angle_refined_deg 1.199 r_angle_other_deg 0.689 r_nbd_other 0.252 r_nbd_refined 0.251 r_symmetry_vdw_other 0.212
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 11.122 r_scbond_it 8.544 r_mcangle_it 6.359 r_mcbond_it 4.389 r_dihedral_angle_1_deg 4.116 r_angle_refined_deg 1.199 r_angle_other_deg 0.689 r_nbd_other 0.252 r_nbd_refined 0.251 r_symmetry_vdw_other 0.212 r_xyhbond_nbd_refined 0.207 r_symmetry_vdw_refined 0.159 r_symmetry_hbond_refined 0.107 r_nbtor_other 0.094 r_chiral_restr 0.069 r_bond_refined_d 0.014 r_bond_other_d 0.012 r_gen_planes_refined 0.005 r_gen_planes_other 0.003 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_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 3701 Nucleic Acid Atoms Solvent Atoms 29 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling SOLVE phasing