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The tetrameric structure of haloalkane dehalogenase DpaA from Paraglaciecola agarilytica NO2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2XT0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277 0.1 M Na HEPES, 4% w/v PEG 400, 2 M (NH4)2SO4
Crystal Properties Matthews coefficient Solvent content 2.63 53.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.385 α = 90 b = 155.506 β = 90 c = 155.611 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 100 PIXEL DECTRIS PILATUS 2M 2015-09-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.918409 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) CC (Half) 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 47.44 100 0.0179 0.998 7.9 1.79 191831 22
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.03 100 0.0161 0.601 1.3
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2xt0 2 47.44 182376 9496 99.83 0.17798 0.17649 0.20586 0.1837 RANDOM 27.229
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] -0.06 0.25 -0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.803 r_dihedral_angle_4_deg 21.643 r_dihedral_angle_3_deg 13.557 r_long_range_B_refined 6.242 r_dihedral_angle_1_deg 6.127 r_long_range_B_other 6.038 r_scangle_other 4.353 r_mcangle_it 4.119 r_mcangle_other 4.119 r_angle_other_deg 3.875
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.803 r_dihedral_angle_4_deg 21.643 r_dihedral_angle_3_deg 13.557 r_long_range_B_refined 6.242 r_dihedral_angle_1_deg 6.127 r_long_range_B_other 6.038 r_scangle_other 4.353 r_mcangle_it 4.119 r_mcangle_other 4.119 r_angle_other_deg 3.875 r_scbond_it 3.454 r_scbond_other 3.453 r_mcbond_it 3.29 r_mcbond_other 3.29 r_angle_refined_deg 1.769 r_chiral_restr 0.122 r_bond_refined_d 0.02 r_gen_planes_other 0.017 r_gen_planes_refined 0.01 r_bond_other_d 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 18745 Nucleic Acid Atoms Solvent Atoms 2008 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing