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Crystal structure of putative thioesterase yhdA from Lactococcus lactis. Northeast Structural Genomics Consortium Target KR113
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VH5 PDB entry 1VH5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 14% PEG 3350, 20% Ethylene glycol, 0.2M CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.11 41.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.948 α = 90 b = 64.056 β = 90 c = 144.657 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 CCD ADSC QUANTUM 4 mirrors 2009-02-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X4A 0.979 NSLS X4A
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 2.24 50 98.7 0.069 27.8 7.6 51899 -3
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 2.24 2.32 87.7 0.41 6.3 7
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 PDB entry 1VH5 2.24 46.18 27547 1385 100 0.2253 0.22366 0.2517 0.25548 0.2656 RANDOM 51.656
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] -4.98 4.53 0.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.95 r_dihedral_angle_3_deg 15.474 r_dihedral_angle_4_deg 9.405 r_dihedral_angle_1_deg 5.916 r_scangle_it 1.327 r_angle_refined_deg 1.065 r_scbond_it 0.897 r_mcangle_it 0.711 r_mcbond_it 0.541 r_nbtor_refined 0.296
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.95 r_dihedral_angle_3_deg 15.474 r_dihedral_angle_4_deg 9.405 r_dihedral_angle_1_deg 5.916 r_scangle_it 1.327 r_angle_refined_deg 1.065 r_scbond_it 0.897 r_mcangle_it 0.711 r_mcbond_it 0.541 r_nbtor_refined 0.296 r_symmetry_vdw_refined 0.186 r_nbd_refined 0.184 r_symmetry_hbond_refined 0.164 r_xyhbond_nbd_refined 0.105 r_chiral_restr 0.071 r_bond_refined_d 0.01 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3917 Nucleic Acid Atoms Solvent Atoms 49 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction ADSC data collection HKL-2000 data reduction SCALEPACK data scaling BALBES phasing