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Structure of the L-2-haloacid dehalogenase from Sulfolobus tokodaii
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QQ5 PDB ENTRY 1QQ5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 0.1M HEPES, 20% PEG6000 PH7.0
Crystal Properties Matthews coefficient Solvent content 1.96 37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.589 α = 90 b = 58.082 β = 97.23 c = 51.192 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 CCD MARRESEARCH 2005-11-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX10.1 SRS PX10.1
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 1.9 23.21 97.6 0.1 16 3.48 27770
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 1.9 1.95 75 0.16 5.7 1.9
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 1QQ5 1.9 23.21 27770 920 100 0.164 0.163 0.1623 0.217 0.2168 RANDOM 23.55
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] 0.33 0.67 -1.71 1.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.106 r_dihedral_angle_3_deg 13.633 r_dihedral_angle_4_deg 13.494 r_scangle_it 6.58 r_dihedral_angle_1_deg 5.184 r_scbond_it 4.328 r_mcangle_it 2.977 r_mcbond_it 1.754 r_angle_refined_deg 1.266 r_chiral_restr 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.106 r_dihedral_angle_3_deg 13.633 r_dihedral_angle_4_deg 13.494 r_scangle_it 6.58 r_dihedral_angle_1_deg 5.184 r_scbond_it 4.328 r_mcangle_it 2.977 r_mcbond_it 1.754 r_angle_refined_deg 1.266 r_chiral_restr 0.09 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3372 Nucleic Acid Atoms Solvent Atoms 305 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing