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X-ray Crystal Structure of Bacillus subtilis RicA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PIH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 100 mM MES pH 6.0, 150 mM NaCl, 65% (vol/vol) MPD
Crystal Properties Matthews coefficient Solvent content 2.75 55.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.491 α = 90 b = 52.212 β = 95.83 c = 27.109 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 93 CCD MARMOSAIC 325 mm CCD 2016-06-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL14-1 1.18076 SSRL BL14-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 99.8 0.141 0.151 0.055 0.99 10.1 7.5 9208 29.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.08 2.12 99.1 0.396 0.428 0.159 0.93 6.9
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 2PIH 2.08 29.83 8761 447 99.71 0.1849 0.183 0.1948 0.2241 0.2328 RANDOM 36.796
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] 0.55 1.4 -1.46 0.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.614 r_dihedral_angle_4_deg 18.153 r_dihedral_angle_3_deg 17.109 r_dihedral_angle_1_deg 4.568 r_angle_refined_deg 1.588 r_angle_other_deg 1.435 r_chiral_restr 0.089 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.614 r_dihedral_angle_4_deg 18.153 r_dihedral_angle_3_deg 17.109 r_dihedral_angle_1_deg 4.568 r_angle_refined_deg 1.588 r_angle_other_deg 1.435 r_chiral_restr 0.089 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 979 Nucleic Acid Atoms Solvent Atoms 52 Heterogen Atoms 1
Software Software Software Name Purpose SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction PHASER phasing