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1.93 A resolution X-ray crystal structure of the transcriptional regulator SrnR from Streptomyces griseus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3F6V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 8.5 293 1 uL of SrnR 12.5 mg mL-1 (in 20 mM TrisHCl PH 7.5, 150 mM NaCl, 1 mM TCEP) were added to 20 uL of volatile oil, immediately followed by 1 uL of precipitant containing 0.2 M calcium acetate hydrate, 0.1 M TrisHCl 8.5, 15 % w/v PEG 4000 (G6 condition of CSSII screening by Molecular Dimensions).
Crystal Properties Matthews coefficient Solvent content 2.36 47.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.358 α = 90 b = 113.358 β = 90 c = 124.943 γ = 120
Symmetry Space Group P 62 2 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 PIXEL DECTRIS PILATUS 6M-F 2019-11-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.97622 PETRA III, EMBL c/o DESY P13 (MX1)
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 1.93 124.94 100 0.126 0.138 0.041 0.999 11.6 11.4 36223 26.8
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 1.93 1.98 100 1.67 1.827 0.541 0.633 1.5 11.7
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3F6V 1.93 51.67 36181 1789 99.975 0.18 0.178 0.1882 0.2167 0.2303 38.772
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] 0.454 0.227 0.454 -1.471
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.194 r_dihedral_angle_4_deg 20.272 r_dihedral_angle_3_deg 15.555 r_lrange_it 7.495 r_lrange_other 7.461 r_dihedral_angle_1_deg 6.172 r_scangle_it 4.527 r_scangle_other 4.526 r_mcangle_it 3.937 r_mcangle_other 3.936
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.194 r_dihedral_angle_4_deg 20.272 r_dihedral_angle_3_deg 15.555 r_lrange_it 7.495 r_lrange_other 7.461 r_dihedral_angle_1_deg 6.172 r_scangle_it 4.527 r_scangle_other 4.526 r_mcangle_it 3.937 r_mcangle_other 3.936 r_scbond_it 2.834 r_scbond_other 2.833 r_mcbond_it 2.489 r_mcbond_other 2.488 r_angle_refined_deg 1.756 r_angle_other_deg 1.45 r_metal_ion_refined 0.257 r_nbd_refined 0.215 r_nbd_other 0.197 r_symmetry_nbd_other 0.196 r_symmetry_xyhbond_nbd_refined 0.16 r_nbtor_refined 0.159 r_xyhbond_nbd_refined 0.151 r_symmetry_nbd_refined 0.145 r_symmetry_nbtor_other 0.093 r_chiral_restr 0.09 r_symmetry_xyhbond_nbd_other 0.014 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3075 Nucleic Acid Atoms Solvent Atoms 347 Heterogen Atoms 19
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing