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Crystal Structure of the complex between S-Adenosyl Methionine and Methanocaldococcus jannaschi Dim1.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3FYD 3FYD, Chain A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.2 293 PEG 8000 (14-16%), 25 MM MES, 50 MM NH2SO4, 7 MM MGCL2, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.37 48.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.468 α = 90 b = 67.021 β = 107.85 c = 62.152 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 IMAGE PLATE RIGAKU RAXIS IV++ Rigaku Varimax Confocal Optics 2008-11-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.5418
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 2.2 22.34 88 0.08 14 6.18 16190 14252 56.2
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 2.2 2.28 85 0.363 3 6.07 1625
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 3FYD, Chain A 2.2 22.18 12810 1431 87.98 0.24328 0.23746 0.2454 0.2951 0.3064 RANDOM 53.392
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] 0.03 -0.83 -0.47 -0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.563 r_dihedral_angle_4_deg 16.456 r_dihedral_angle_3_deg 15.968 r_dihedral_angle_1_deg 5.289 r_scangle_it 2.168 r_scbond_it 1.576 r_angle_refined_deg 1.139 r_mcangle_it 0.933 r_mcbond_it 0.468 r_chiral_restr 0.079
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.563 r_dihedral_angle_4_deg 16.456 r_dihedral_angle_3_deg 15.968 r_dihedral_angle_1_deg 5.289 r_scangle_it 2.168 r_scbond_it 1.576 r_angle_refined_deg 1.139 r_mcangle_it 0.933 r_mcbond_it 0.468 r_chiral_restr 0.079 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2105 Nucleic Acid Atoms Solvent Atoms 125 Heterogen Atoms 32
Software Software Software Name Purpose CrystalClear data collection PHENIX model building REFMAC refinement d*TREK data reduction d*TREK data scaling PHENIX phasing