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Crystal structure of Regulator of Proteinase B RopB complexed with SIP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5DL2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 295 2.7 M potassium formate, 0.1 M Tris pH 7.3, 1% PEG2000, 0.15 M potassium chloride and 1 mM EDTA
Crystal Properties Matthews coefficient Solvent content 4.14 70.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.211 α = 90 b = 94.211 β = 90 c = 179.957 γ = 120
Symmetry Space Group P 32 1 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 PILATUS3 S 6M 2017-09-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.1158 ALS 8.3.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 3.3 30 99.5 0.065 1 24.5 20 13969
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.3 3.41 1.772 0.917
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 5DL2 3.3 29.17 13279 690 99.4 0.23532 0.23358 0.2316 0.26598 0.2552 RANDOM 174.789
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] 1.87 1.87 -3.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.964 r_long_range_B_refined 26.49 r_long_range_B_other 26.489 r_scangle_other 19.948 r_mcangle_it 18.763 r_mcangle_other 18.759 r_dihedral_angle_3_deg 16.719 r_dihedral_angle_4_deg 15.408 r_scbond_it 13.214 r_scbond_other 13.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.964 r_long_range_B_refined 26.49 r_long_range_B_other 26.489 r_scangle_other 19.948 r_mcangle_it 18.763 r_mcangle_other 18.759 r_dihedral_angle_3_deg 16.719 r_dihedral_angle_4_deg 15.408 r_scbond_it 13.214 r_scbond_other 13.21 r_mcbond_it 12.156 r_mcbond_other 12.155 r_dihedral_angle_1_deg 5.107 r_angle_other_deg 1.197 r_angle_refined_deg 1.014 r_chiral_restr 0.057 r_bond_refined_d 0.009 r_bond_other_d 0.006 r_gen_planes_refined 0.005 r_gen_planes_other 0.004 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 3855 Nucleic Acid Atoms Solvent Atoms 13 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing