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Crystal structure of cold-adapted haloalkane dehalogenase DpcA from Psychrobacter cryohalolentis K5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1B6G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.88 293 0.2 M ammonium acetate, 30%(w/v) PEG 4000 and 0.1 M sodium acetate trihydrate pH 4.6 and with the addition of 0.6 ul of 0.1M L-proline (Additive Screen kit, Hampton Research) to the crystallization drop
Crystal Properties Matthews coefficient Solvent content 2.04 39.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.332 α = 90 b = 79.451 β = 94.98 c = 43.489 γ = 90
Symmetry Space Group P 1 21 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 RAYONIX MX-225 Sagitally bended Si111 crystal 2012-02-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.978260 BESSY 14.2
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 1.05 20 92.2 0.05 39.7 5.7 120315 16.716
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 1.05 1.09 56.2 0.307 3.4
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 1B6G 1.05 20 114202 6066 91.98 0.11139 0.11033 0.11 0.13151 0.1314 RANDOM 8.671
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.671 r_sphericity_free 22.761 r_dihedral_angle_4_deg 16.682 r_dihedral_angle_3_deg 12.244 r_sphericity_bonded 7.178 r_dihedral_angle_1_deg 6.086 r_long_range_B_refined 2.693 r_long_range_B_other 2.693 r_rigid_bond_restr 2.273 r_angle_refined_deg 1.634
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.671 r_sphericity_free 22.761 r_dihedral_angle_4_deg 16.682 r_dihedral_angle_3_deg 12.244 r_sphericity_bonded 7.178 r_dihedral_angle_1_deg 6.086 r_long_range_B_refined 2.693 r_long_range_B_other 2.693 r_rigid_bond_restr 2.273 r_angle_refined_deg 1.634 r_scangle_other 1.322 r_scbond_it 1.083 r_scbond_other 1.082 r_angle_other_deg 1.03 r_mcangle_it 1.023 r_mcangle_other 1.022 r_mcbond_it 0.71 r_mcbond_other 0.71 r_chiral_restr 0.097 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_gen_planes_other 0.003 r_bond_other_d 0.002 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2465 Nucleic Acid Atoms Solvent Atoms 576 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing