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Crystal structure of the R236E mutant of Methylophilus methylotrophus ETF
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1O97
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.2 limited digest with trypsin, 2.0 M sodium phosphate, pH 6.2, VAPOR DIFFUSION
Crystal Properties Matthews coefficient Solvent content 2.65 53.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.692 α = 90 b = 116.692 β = 90 c = 84.412 γ = 120
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 ADSC QUANTUM 210 2005-04-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2 20 99.9 0.062 11.2 4.5 41782 41782
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 FOURIER SYNTHESIS THROUGHOUT 1O97 2 19.91 41782 2209 99.95 0.15492 0.15326 0.1642 0.18607 0.1967 RANDOM 22.176
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] 0.16 0.08 0.16 -0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.669 r_dihedral_angle_4_deg 18.238 r_dihedral_angle_3_deg 13.149 r_dihedral_angle_1_deg 6.15 r_scangle_it 2.199 r_scbond_it 1.409 r_angle_refined_deg 1.301 r_mcangle_it 0.889 r_angle_other_deg 0.797 r_mcbond_it 0.608
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.669 r_dihedral_angle_4_deg 18.238 r_dihedral_angle_3_deg 13.149 r_dihedral_angle_1_deg 6.15 r_scangle_it 2.199 r_scbond_it 1.409 r_angle_refined_deg 1.301 r_mcangle_it 0.889 r_angle_other_deg 0.797 r_mcbond_it 0.608 r_symmetry_vdw_other 0.219 r_nbd_refined 0.199 r_nbd_other 0.18 r_nbtor_refined 0.167 r_symmetry_hbond_refined 0.147 r_xyhbond_nbd_refined 0.133 r_mcbond_other 0.109 r_nbtor_other 0.081 r_chiral_restr 0.076 r_symmetry_vdw_refined 0.068 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4243 Nucleic Acid Atoms Solvent Atoms 632 Heterogen Atoms 76
Software Software Software Name Purpose REFMAC refinement DNA data collection DENZO data reduction SCALEPACK data scaling