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Crystal Structure Analysis of Rif16 in complex with R-L
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4OQS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8.5 277 Magnesium chloride hexahydrate, PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.16 42.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.082 α = 90 b = 70.709 β = 94 c = 80.975 γ = 90
Symmetry Space Group P 1 21 1
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 SIEMENS-NICOLET mirrors 2017-11-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.976 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.55 50 98.7 0.11 0.12 0.049 5.7 5.8 12806
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 2.55 2.64 99.3 0.555 0.609 0.247 0.833 5.7
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 (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 4OQS 2.6 35.38 11248 580 96.22 0.2085 0.2052 0.21 0.2714 0.2688 RANDOM 37.57
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] 0.33 0.19 -0.59 0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.69 r_dihedral_angle_4_deg 26.466 r_dihedral_angle_3_deg 22.456 r_dihedral_angle_1_deg 6.278 r_angle_refined_deg 1.704 r_angle_other_deg 0.924 r_chiral_restr 0.099 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_bond_other_d 0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.69 r_dihedral_angle_4_deg 26.466 r_dihedral_angle_3_deg 22.456 r_dihedral_angle_1_deg 6.278 r_angle_refined_deg 1.704 r_angle_other_deg 0.924 r_chiral_restr 0.099 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_bond_other_d 0.005 r_gen_planes_other 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2868 Nucleic Acid Atoms Solvent Atoms 64 Heterogen Atoms 97
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PDB_EXTRACT data extraction HKL-3000 data reduction REFMAC phasing