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Crystal Structure of the Native Form of Uroporphyrin III C-methyl transferase from Thermus thermophilus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1CBF PDB Entry 1CBF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 291 Citrate, PEG 20000, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.42 48.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.5 α = 90 b = 63.568 β = 90 c = 131.902 γ = 90
Symmetry Space Group P 21 21 21
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 VII Mirrors 2003-12-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007
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 1.97 31.78 99.8 0.039 18.8 3.6 36786 36786 25.4
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 1.97 2.04 99.9 0.494 1.65 3.53 3629
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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB Entry 1CBF 1.97 31.78 35288 35288 1751 95.9 0.199 0.199 0.1993 0.227 0.2274 RANDOM 41.9
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] 2.31 2.08 -4.39
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 24.6 c_scangle_it 6.5 c_scbond_it 4.97 c_mcangle_it 4.41 c_mcbond_it 3.5 c_angle_deg 1.6 c_improper_angle_d 1 c_bond_d 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3479 Nucleic Acid Atoms Solvent Atoms 244 Heterogen Atoms 23
Software Software Software Name Purpose CNS refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing