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Structure of the lactate racemase apoprotein from Thermoanaerobacterium thermosaccharolyticum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other MAD-SOLVED PARTIAL MODEL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 HANGING DROP. RESERVOIR: 22%(W/V) PEGMME 5000, 0.2 M AMMONIUM SULFATE, 0.1 M MES PH 6.5, 3%(V/V) ETHYLENE GLYCOL. DROP: 1 MICROL PROTEIN AND 1 MICROL RESERVOIR.
Crystal Properties Matthews coefficient Solvent content 2.06 40.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.41 α = 90 b = 223.25 β = 90 c = 46.14 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315r TWO MIRRORS ARE USED FOR VERTICAL FOCUSSING. THEY ALSO ALLOW TO REJECT HIGH ORDER HARMONICS FOUND IN THE WHITE BEAM. 2011-02-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A ESRF BM30A
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 1.8 45 97 0.06 16 4.6 73824 29.6
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 1.8 2 91 0.33 4.1 4.1
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 MAD-SOLVED PARTIAL MODEL 1.8 114.96 70103 3721 97.11 0.18407 0.18169 0.1857 0.22933 0.2318 RANDOM 18.72
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] -0.53 1.22 -0.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.051 r_dihedral_angle_4_deg 20.646 r_dihedral_angle_3_deg 15.775 r_dihedral_angle_1_deg 6.091 r_scangle_it 4.839 r_scbond_it 3.007 r_mcangle_it 1.817 r_angle_refined_deg 1.729 r_mcbond_it 1.053 r_angle_other_deg 0.971
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.051 r_dihedral_angle_4_deg 20.646 r_dihedral_angle_3_deg 15.775 r_dihedral_angle_1_deg 6.091 r_scangle_it 4.839 r_scbond_it 3.007 r_mcangle_it 1.817 r_angle_refined_deg 1.729 r_mcbond_it 1.053 r_angle_other_deg 0.971 r_mcbond_other 0.318 r_chiral_restr 0.106 r_bond_refined_d 0.02 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6459 Nucleic Acid Atoms Solvent Atoms 587 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling Auto-Rickshaw phasing