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Crystal Structure of Moonlighting GAPDH protein of Lactobacillus gasseri
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3LVF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 298 0.1 M sodium cacodylate pH 6.5, 16% (w/v) PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.71 54.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.922 α = 90 b = 114.922 β = 90 c = 118.62 γ = 90
Symmetry Space Group I 41 2 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 VERTICALLY COLLIMATING PREMIRROR, TOROIDAL FOCUSING MIRROR 2016-11-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13C1 0.97622 NSRRC BL13C1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.88 30 98.8 0.067 0.07 0.02 41.7 12 32168 32
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.88 1.95 94.8 0.546 0.572 0.165 0.96 3.7 10.5
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 (All) 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 3LVF 1.88 29.673 32038 1625 98.469 0.138 0.1344 0.1344 0.217 0.2172 RANDOM 44.881
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] -0.676 -0.676 1.352
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.332 r_dihedral_angle_3_deg 15.383 r_dihedral_angle_4_deg 15.22 r_lrange_it 7.845 r_dihedral_angle_1_deg 7.762 r_scangle_it 7.539 r_scbond_it 7.192 r_rigid_bond_restr 6.538 r_mcangle_it 6.164 r_mcbond_it 5.384
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.332 r_dihedral_angle_3_deg 15.383 r_dihedral_angle_4_deg 15.22 r_lrange_it 7.845 r_dihedral_angle_1_deg 7.762 r_scangle_it 7.539 r_scbond_it 7.192 r_rigid_bond_restr 6.538 r_mcangle_it 6.164 r_mcbond_it 5.384 r_angle_refined_deg 1.404 r_nbtor_refined 0.316 r_nbd_refined 0.219 r_symmetry_xyhbond_nbd_refined 0.191 r_xyhbond_nbd_refined 0.161 r_symmetry_nbd_refined 0.154 r_chiral_restr 0.099 r_gen_planes_refined 0.011 r_bond_refined_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2534 Nucleic Acid Atoms Solvent Atoms 247 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing