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Mutant glyceraldehyde dehydrogenase (F34M+S405N) from Thermoplasma acidophilum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5IZD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 295 0.1 M sodium acetate pH 4.6, 40%(v/v) PEG 200
Crystal Properties Matthews coefficient Solvent content 2.5 50.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.071 α = 90 b = 158.423 β = 91.57 c = 130.05 γ = 90
Symmetry Space Group C 1 2 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 PIXEL DECTRIS PILATUS 6M 2014-03-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.918409 BESSY 14.1
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 2.1 44.63 99.6 0.092 12.13 3.81 126605 32.88
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.23 98.7 2.32
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 5IZD 2.1 44.63 120272 6331 99.56 0.17843 0.17596 0.188 0.22631 0.2338 RANDOM 46.093
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] 1.1 -1.37 -1.87 0.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.813 r_dihedral_angle_4_deg 18.329 r_dihedral_angle_3_deg 13.968 r_dihedral_angle_1_deg 6.621 r_long_range_B_refined 4.513 r_long_range_B_other 4.448 r_scangle_other 2.314 r_mcangle_it 1.708 r_mcangle_other 1.708 r_angle_refined_deg 1.685
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.813 r_dihedral_angle_4_deg 18.329 r_dihedral_angle_3_deg 13.968 r_dihedral_angle_1_deg 6.621 r_long_range_B_refined 4.513 r_long_range_B_other 4.448 r_scangle_other 2.314 r_mcangle_it 1.708 r_mcangle_other 1.708 r_angle_refined_deg 1.685 r_scbond_it 1.505 r_scbond_other 1.504 r_mcbond_it 1.14 r_mcbond_other 1.135 r_angle_other_deg 1.042 r_chiral_restr 0.103 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15047 Nucleic Acid Atoms Solvent Atoms 578 Heterogen Atoms
Software Software Software Name Purpose XDS data reduction XDS data scaling MOLREP phasing REFMAC refinement