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Crystal structure of protein MJ0408 from Methanococcus jannaschii, Pfam DUF372
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2IEC pdb entry 2IEC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 298 24% PEG-3350, Tris-HCL, 0.2 M Ammonium Sulfate, pH 4.6, Vapor diffusion, Sitting drop, temperature 298K, VAPOR DIFFUSION, SITTING DROP
Crystal Properties Matthews coefficient Solvent content 2.11 41.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.693 α = 90 b = 46.27 β = 118.54 c = 79.276 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 2006-12-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE OTHER
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.89 50 97.4 0.066 0.051 8.9 3.6 37996 37996
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.89 1.96 77.8 0.337 0.328 3 2.9 3018
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 (All) 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 pdb entry 2IEC 1.89 27 37966 37966 1913 97.32 0.175 0.175 0.173 0.1718 0.224 0.2257 RANDOM 20.516
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 -0.11 -0.23 0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.519 r_dihedral_angle_4_deg 16.872 r_dihedral_angle_3_deg 13.768 r_dihedral_angle_1_deg 5.726 r_scangle_it 3.049 r_scbond_it 2.073 r_angle_refined_deg 1.446 r_mcangle_it 1.081 r_mcbond_it 0.706 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.519 r_dihedral_angle_4_deg 16.872 r_dihedral_angle_3_deg 13.768 r_dihedral_angle_1_deg 5.726 r_scangle_it 3.049 r_scbond_it 2.073 r_angle_refined_deg 1.446 r_mcangle_it 1.081 r_mcbond_it 0.706 r_nbtor_refined 0.302 r_nbd_refined 0.201 r_symmetry_vdw_refined 0.199 r_xyhbond_nbd_refined 0.135 r_chiral_restr 0.098 r_symmetry_hbond_refined 0.089 r_bond_refined_d 0.016 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3995 Nucleic Acid Atoms Solvent Atoms 339 Heterogen Atoms 70
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction MOLREP phasing