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Crystal structure of C2498 2'-O-ribose methyltransferase RlmM from Escherichia coli
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other MODEL OBTAINED FROM K2PTCL4 DERIVATIVE CRYSTAL DATA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 0.3 M AMMONIUM TARTRATE DIBASIC PH 7.0, 20% PEG 3350, 3.0% DEXTRAN SULFATE SODIUM SALT
Crystal Properties Matthews coefficient Solvent content 2.4 48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.09 α = 90 b = 92.09 β = 90 c = 83.09 γ = 120
Symmetry Space Group P 31 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 100 CCD MARRESEARCH SX-165 2012-03-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I911-2 MAX II I911-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.95 28.77 99.8 0.06 25 7.3 30022 2 33.02
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2 96 0.87 3.5 6.3
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT MODEL OBTAINED FROM K2PTCL4 DERIVATIVE CRYSTAL DATA 1.95 28.769 1.99 30022 1502 99.77 0.1707 0.1688 0.164 0.2062 0.1989 34.12
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] -1.5099 -1.5099 3.0198
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.001 f_angle_d 1.072 f_chiral_restr 0.074 f_bond_d 0.008 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2880 Nucleic Acid Atoms Solvent Atoms 195 Heterogen Atoms 134
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing