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Crystal structure of a methyltransferase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5E1D PDB entry 5E1D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 30% PEG2000, 0.1 M potassium thiocyanate
Crystal Properties Matthews coefficient Solvent content 2.51 50.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.359 α = 90 b = 44.359 β = 90 c = 262.058 γ = 90
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 RAYONIX MX-300 2016-01-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.97949 CLSI 08ID-1
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 1.2 31.14 96 0.074 0.081 0.032 0.998 11 6.1 150535
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 1.2 1.22 93.2 0.973 1.056 0.404 0.675 6.6 7191
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 5E1D 1.2 31.1 145394 4983 95.91 0.1548 0.154 0.1627 0.1778 0.1842 16.091
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] -0.35 -0.35 0.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.412 r_sphericity_free 18.025 r_dihedral_angle_4_deg 12.089 r_dihedral_angle_3_deg 11.493 r_sphericity_bonded 8.282 r_dihedral_angle_1_deg 6.176 r_mcangle_it 2.706 r_rigid_bond_restr 2.7 r_mcbond_it 2.024 r_mcbond_other 2.024
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.412 r_sphericity_free 18.025 r_dihedral_angle_4_deg 12.089 r_dihedral_angle_3_deg 11.493 r_sphericity_bonded 8.282 r_dihedral_angle_1_deg 6.176 r_mcangle_it 2.706 r_rigid_bond_restr 2.7 r_mcbond_it 2.024 r_mcbond_other 2.024 r_angle_refined_deg 1.823 r_angle_other_deg 0.921 r_chiral_restr 0.12 r_bond_refined_d 0.016 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3509 Nucleic Acid Atoms Solvent Atoms 314 Heterogen Atoms 154
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction HKL-3000 data reduction PHASER phasing