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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 3350 (18%), 25 mM MES, 50 mM Na2HPO4, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.29 46.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.384 α = 90 b = 72.274 β = 91.87 c = 95.883 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 2008-04-23 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 2.15 32.77 94.9 0.091 12.4 6.62 30159 28619 37.9
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) 2.15 2.23 91.9 0.361 4.7 6.65 3014
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT composite model consisting of monomers from pdb entries 1QYR, 2H1R and 1ZQ9 2.15 32 25730 2873 94.89 0.20946 0.20237 0.2101 0.27332 RANDOM 36.407
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] -2.26 -1.33 3.05 -0.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.084 r_dihedral_angle_4_deg 20.115 r_dihedral_angle_3_deg 15.153 r_dihedral_angle_1_deg 5.622 r_scangle_it 4.135 r_scbond_it 2.692 r_mcangle_it 1.68 r_angle_refined_deg 1.123 r_mcbond_it 0.823 r_nbtor_refined 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.084 r_dihedral_angle_4_deg 20.115 r_dihedral_angle_3_deg 15.153 r_dihedral_angle_1_deg 5.622 r_scangle_it 4.135 r_scbond_it 2.692 r_mcangle_it 1.68 r_angle_refined_deg 1.123 r_mcbond_it 0.823 r_nbtor_refined 0.3 r_nbd_refined 0.187 r_symmetry_vdw_refined 0.167 r_symmetry_hbond_refined 0.158 r_xyhbond_nbd_refined 0.131 r_chiral_restr 0.081 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other 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 4307 Nucleic Acid Atoms Solvent Atoms 292 Heterogen Atoms 50
Software Software Software Name Purpose CrystalClear data collection PHASER phasing REFMAC refinement CrystalClear data reduction CrystalClear data scaling