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Crystal Structure of Dim1 from the thermophilic archeon, Methanocaldococcus jannaschi
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QYR composite model consisting of monomers from pdb entries 1QYR, 2H1R and 1ZQ9 experimental model PDB 2H1R composite model consisting of monomers from pdb entries 1QYR, 2H1R and 1ZQ9 experimental model PDB 1ZQ9 composite model consisting of monomers from pdb entries 1QYR, 2H1R and 1ZQ9
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 2.57 52.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.236 α = 90 b = 65.906 β = 108.1 c = 61.932 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 2008-05-03 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 1.75 33.1 94.4 0.038 29.1 7.06 31119 29365 38.9
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) 1.75 1.81 91.1 0.294 4.9 6.98 3079
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT composite model consisting of monomers from pdb entries 1QYR, 2H1R and 1ZQ9 1.75 22 31106 26413 2926 94.37 0.18126 0.17624 0.2098 0.22643 RANDOM 43.95
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] -0.07 -0.42 -0.48 0.3
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_2_deg 32.708 f_dihedral_angle_4_deg 14.768 f_dihedral_angle_3_deg 14.475 f_scangle_it 9.584 f_scbond_it 8.044 f_dihedral_angle_1_deg 5.679 f_mcangle_it 4.87 f_mcbond_it 4.041 f_angle_refined_deg 1.133 f_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_2_deg 32.708 f_dihedral_angle_4_deg 14.768 f_dihedral_angle_3_deg 14.475 f_scangle_it 9.584 f_scbond_it 8.044 f_dihedral_angle_1_deg 5.679 f_mcangle_it 4.87 f_mcbond_it 4.041 f_angle_refined_deg 1.133 f_nbtor_refined 0.304 f_nbd_refined 0.197 f_symmetry_vdw_refined 0.188 f_symmetry_hbond_refined 0.133 f_xyhbond_nbd_refined 0.127 f_chiral_restr 0.09 f_bond_refined_d 0.011 f_gen_planes_refined 0.005 f_bond_other_d f_angle_other_deg f_gen_planes_other f_nbd_other f_nbtor_other f_xyhbond_nbd_other f_metal_ion_refined f_metal_ion_other f_symmetry_vdw_other f_symmetry_hbond_other f_symmetry_metal_ion_refined f_symmetry_metal_ion_other f_mcbond_other f_rigid_bond_restr f_sphericity_free f_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2177 Nucleic Acid Atoms Solvent Atoms 333 Heterogen Atoms 25
Software Software Software Name Purpose CrystalClear data collection PHASER phasing PHENIX refinement CrystalClear data reduction CrystalClear data scaling