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Structure of a Group I haloacid dehalogenase from Pseudomonas putida strain PP3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 hanging drop 6 298 25% PEG 3350 w/v, 0.4M Li2SO4, 0.1M Bis-Tris pH 6.0, hanging drop, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.24 40.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.323 α = 90 b = 111.864 β = 93.71 c = 75.181 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 IMAGE PLATE RIGAKU RAXIS Mirrors 2006-02-20 SINGLE WAVELENGTH 2 1 x-ray 100 CCD ADSC QUANTUM 315 Vertical focusing mirror 2006-02-20 MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418 2 SYNCHROTRON SSRL BEAMLINE BL9-1 0.97929, 0.97925, 0.91837 SSRL BL9-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1,2 2.3 75.024 96.3 0.118 0.118 6.1 2.5 48240
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.3 2.42 81 0.454 0.454 1.6 2 5900
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MAD THROUGHOUT 2.3 38.15 45759 2457 96.23 0.18463 0.18117 0.25018 0.2129 RANDOM 24.182
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 -0.06 0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.176 r_dihedral_angle_4_deg 23.57 r_dihedral_angle_3_deg 16.329 r_dihedral_angle_1_deg 6.219 r_scangle_it 2.234 r_mcangle_it 2.215 r_scbond_it 1.52 r_mcbond_it 1.482 r_angle_refined_deg 1.447 r_nbtor_refined 0.299
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.176 r_dihedral_angle_4_deg 23.57 r_dihedral_angle_3_deg 16.329 r_dihedral_angle_1_deg 6.219 r_scangle_it 2.234 r_mcangle_it 2.215 r_scbond_it 1.52 r_mcbond_it 1.482 r_angle_refined_deg 1.447 r_nbtor_refined 0.299 r_symmetry_vdw_refined 0.217 r_nbd_refined 0.204 r_symmetry_hbond_refined 0.176 r_xyhbond_nbd_refined 0.17 r_chiral_restr 0.093 r_bond_refined_d 0.012 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9435 Nucleic Acid Atoms Solvent Atoms 449 Heterogen Atoms 80
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling SOLVE phasing RESOLVE phasing REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection