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Mth0212 with two bound manganese ions
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3FZI PDB ENTRY 3FZI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 reservoir solution: 10% (w/v) PEG 20000, 100mM MES-NaOH pH 6.5; protein solution: 600mM NaCl, 20mM HEPES-KOH pH 7.6, 2mM DTT; soaking in 6% (w/v) PEG 20000, 23% (v/v) glycerol, 60mM MES-NaOH pH 6.5, 200mM MnCl2, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.38 48.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.381 α = 90 b = 56.381 β = 90 c = 162.932 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 130 IMAGE PLATE MAR scanner 345 mm plate 2007-02-28 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 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 2.6 50 96.6 0.095 17 6.5 8864
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.6 2.69 0.351 2.4
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 PDB ENTRY 3FZI 2.6 48.83 8440 415 98.39 0.193 0.19 0.1902 0.252 0.2471 RANDOM 32.202
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] 1.95 0.97 1.95 -2.92
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.373 r_dihedral_angle_3_deg 19.946 r_dihedral_angle_4_deg 18.011 r_dihedral_angle_1_deg 6.59 r_scangle_it 1.868 r_angle_refined_deg 1.355 r_scbond_it 1.121 r_mcangle_it 1.031 r_mcbond_it 0.573 r_nbtor_refined 0.315
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.373 r_dihedral_angle_3_deg 19.946 r_dihedral_angle_4_deg 18.011 r_dihedral_angle_1_deg 6.59 r_scangle_it 1.868 r_angle_refined_deg 1.355 r_scbond_it 1.121 r_mcangle_it 1.031 r_mcbond_it 0.573 r_nbtor_refined 0.315 r_symmetry_vdw_refined 0.221 r_nbd_refined 0.199 r_xyhbond_nbd_refined 0.161 r_symmetry_hbond_refined 0.113 r_chiral_restr 0.099 r_bond_refined_d 0.01 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2147 Nucleic Acid Atoms Solvent Atoms 71 Heterogen Atoms 13
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction MAR345 data collection HKL-2000 data reduction HKL-2000 data scaling