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Crystal structure of rRNA methyltransferase Erm38 in complex with sinefungin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7F8A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 1.0 M succinic acid pH 7, 5% glycerol
Crystal Properties Matthews coefficient Solvent content 2.67 53.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.018 α = 90 b = 78.018 β = 90 c = 101.536 γ = 90
Symmetry Space Group P 42 21 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 EIGER X 9M 2018-02-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.98 SOLEIL PROXIMA 2
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 2.248 48.47 99.8 0.079 0.08 0.016 1 31.3 25.9 15503 48.43
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 2.25 2.32 97.5 0.8 0.818 0.167 0.93 23.3
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 7F8A 2.248 48.47 15465 761 99.7 0.2166 0.2144 0.2041 0.2573 0.2356 RANDOM 43.25
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] 4.4206 4.4206 -8.8412
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 13.04 t_omega_torsion 3.09 t_angle_deg 0.88 t_bond_d 0.008 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 13.04 t_omega_torsion 3.09 t_angle_deg 0.88 t_bond_d 0.008 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1884 Nucleic Acid Atoms Solvent Atoms 136 Heterogen Atoms 35
Software Software Software Name Purpose Aimless data scaling BUSTER refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing