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Crystal Structure of the Fluoroacetate Dehalogenase D104 mutant from Burkholderia sp. FA1 in complex with fluoroacetate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Y37 PDB ENTRY 1Y37
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 277 20%(w/v) PEG 8000, 100mM Tris-HCl buffer pH 8.5, 40mM MgCl2, 100mM fluoroacetate , VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.28 45.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.497 α = 90 b = 85.065 β = 90 c = 136.354 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 CCD ADSC QUANTUM 210 2005-05-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A Photon Factory AR-NW12A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.15 50 99.3 220817 219357 2 2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1Y37 1.2 37.72 2 174938 19301 99.94 0.1767 0.1767 0.17579 0.18492 0.1706 RANDOM 8.711
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] 0.16 0.13 -0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.993 r_dihedral_angle_4_deg 16 r_dihedral_angle_3_deg 10.43 r_dihedral_angle_1_deg 5.05 r_scangle_it 1.992 r_scbond_it 1.316 r_angle_refined_deg 1.142 r_mcangle_it 0.84 r_mcbond_it 0.508 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.993 r_dihedral_angle_4_deg 16 r_dihedral_angle_3_deg 10.43 r_dihedral_angle_1_deg 5.05 r_scangle_it 1.992 r_scbond_it 1.316 r_angle_refined_deg 1.142 r_mcangle_it 0.84 r_mcbond_it 0.508 r_nbtor_refined 0.31 r_nbd_refined 0.199 r_symmetry_vdw_refined 0.177 r_xyhbond_nbd_refined 0.107 r_chiral_restr 0.081 r_symmetry_hbond_refined 0.053 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 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 4634 Nucleic Acid Atoms Solvent Atoms 561 Heterogen Atoms 17
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling