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BshB from Bacillus subtilis complexed with citrate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2IXD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 10% PEG 3350, 100 mM sodium citrate tribasic, 10 mM HEPES, 25 mM NaCl, pH 8.3
Crystal Properties Matthews coefficient Solvent content 3.01 63.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.538 α = 90 b = 98.538 β = 90 c = 184.877 γ = 120
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 2014-12-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.0782 APS 21-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 1.853 77.49 100 0.105 0.109 0.029 16.8 14.4 29650
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.853 1.95 100 1.485 1.485 1.538 0.399 0.5 14.8
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 2IXD 1.853 77.48 28202 1445 99.97 0.1732 0.1715 0.1829 0.2049 0.2143 RANDOM 36.579
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] 1.13 0.56 1.13 -3.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.874 r_dihedral_angle_4_deg 16.962 r_dihedral_angle_3_deg 14.28 r_dihedral_angle_1_deg 5.875 r_angle_refined_deg 1.344 r_angle_other_deg 1.314 r_chiral_restr 0.067 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.874 r_dihedral_angle_4_deg 16.962 r_dihedral_angle_3_deg 14.28 r_dihedral_angle_1_deg 5.875 r_angle_refined_deg 1.344 r_angle_other_deg 1.314 r_chiral_restr 0.067 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1803 Nucleic Acid Atoms Solvent Atoms 164 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction MOSFLM data reduction PHASER phasing