☰ Navigation Tabs
Crystal structure of a thermostable alanine racemase from Thermoanaerobacter tengcongensis MB4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SFT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 289 22% PEG 4000, 0.1M Bis-Tris pH7.0
Crystal Properties Matthews coefficient Solvent content 2.75 55.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.843 α = 90 b = 73.077 β = 90 c = 218.746 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 IV++ 2014-04-07 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 2.7 50 96.6 0.073 7.3 5.2 26832
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 2.7 2.75 83.4 0.261 2.7 3.4
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 1SFT 2.7 50 25425 1353 96.38 0.2155 0.2136 0.2145 0.2524 0.2514 RANDOM 45.735
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] -2.73 -0.06 2.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.796 r_dihedral_angle_4_deg 16.63 r_dihedral_angle_3_deg 14.095 r_dihedral_angle_1_deg 5.378 r_mcangle_it 1.859 r_mcbond_it 1.057 r_mcbond_other 1.057 r_angle_refined_deg 0.986 r_angle_other_deg 0.66 r_chiral_restr 0.051
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.796 r_dihedral_angle_4_deg 16.63 r_dihedral_angle_3_deg 14.095 r_dihedral_angle_1_deg 5.378 r_mcangle_it 1.859 r_mcbond_it 1.057 r_mcbond_other 1.057 r_angle_refined_deg 0.986 r_angle_other_deg 0.66 r_chiral_restr 0.051 r_bond_refined_d 0.004 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6212 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction PHASER phasing