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Crystal structure of native ribT from Bacillus subtilis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5XXR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 80% 2.7M sodium malonate, 20% 2.1M Malic acid
Crystal Properties Matthews coefficient Solvent content 2.13 42.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.58 α = 90 b = 57.444 β = 90 c = 74.528 γ = 90
Symmetry Space Group P 21 21 21
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 225 mm CCD Mirror 2015-11-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.95372 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 2.08 50 92.6 0.077 0.94 18.7 4.5 13197 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.08 2.12 56.7 0.38 0.74 2.03 2.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 5XXR 2.09 34.95 11888 1308 92.23 0.20662 0.19974 0.2038 0.26691 0.2678 RANDOM 39.667
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] -1.61 -2.19 3.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.387 r_dihedral_angle_3_deg 14.255 r_dihedral_angle_4_deg 11.784 r_dihedral_angle_1_deg 6.03 r_long_range_B_refined 5.519 r_long_range_B_other 5.484 r_scangle_other 3.466 r_mcangle_other 3.163 r_mcangle_it 3.159 r_scbond_it 2.096
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.387 r_dihedral_angle_3_deg 14.255 r_dihedral_angle_4_deg 11.784 r_dihedral_angle_1_deg 6.03 r_long_range_B_refined 5.519 r_long_range_B_other 5.484 r_scangle_other 3.466 r_mcangle_other 3.163 r_mcangle_it 3.159 r_scbond_it 2.096 r_scbond_other 2.093 r_mcbond_it 1.976 r_mcbond_other 1.966 r_angle_refined_deg 1.338 r_angle_other_deg 0.903 r_chiral_restr 0.071 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1892 Nucleic Acid Atoms Solvent Atoms 89 Heterogen Atoms 121
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing