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Crystal structure of haloalkane dehalogenase LinB from Sphingobium sp. MI1205
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1CV2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 278 100mM Tris-HCl (pH 8.0), 20% (w/v) PEG 4000, 200mM CaCl2, VAPOR DIFFUSION, SITTING DROP, temperature 278K
Crystal Properties Matthews coefficient Solvent content 1.96 37.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.404 α = 90 b = 72.146 β = 90 c = 73.492 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 2008-06-07
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0000 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 1.6 20 36060
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 1CV2 1.6 20 34221 1797 99.9 0.16026 0.15863 0.1672 0.19101 0.1943 RANDOM 8.176
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] -0.52 0.07 0.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.247 r_dihedral_angle_4_deg 14.098 r_dihedral_angle_3_deg 13.328 r_dihedral_angle_1_deg 5.445 r_scangle_it 2.785 r_scbond_it 1.716 r_angle_refined_deg 1.371 r_mcangle_it 0.974 r_mcbond_it 0.81 r_nbtor_refined 0.317
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.247 r_dihedral_angle_4_deg 14.098 r_dihedral_angle_3_deg 13.328 r_dihedral_angle_1_deg 5.445 r_scangle_it 2.785 r_scbond_it 1.716 r_angle_refined_deg 1.371 r_mcangle_it 0.974 r_mcbond_it 0.81 r_nbtor_refined 0.317 r_symmetry_vdw_refined 0.213 r_symmetry_hbond_refined 0.211 r_nbd_refined 0.205 r_xyhbond_nbd_refined 0.143 r_chiral_restr 0.092 r_metal_ion_refined 0.076 r_symmetry_metal_ion_refined 0.012 r_bond_refined_d 0.01 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2332 Nucleic Acid Atoms Solvent Atoms 358 Heterogen Atoms 21
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling