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The Effect of Deuteration on Protein Structure A High Resolution Comparison of Hydrogenous and Perdeuterated Haloalkane Dehalogenase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1B6G PDB entry 1B6G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 293 2.6M ammonium sulfate, 0.1M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.92 36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.363 α = 90 b = 71.093 β = 90 c = 40.035 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 IMAGE PLATE RIGAKU RAXIS IV 2006-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
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 1.53 28.76 83.1 0.077 9.4 3.52 41347 1.8
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) 1.55 1.62 16.3 0.352 1.8 2.3
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION rigid body refinement THROUGHOUT PDB entry 1B6G 1.55 28.76 36432 1959 96.15 0.19143 0.18922 0.2026 0.23135 0.2439 RANDOM 30.31
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] 0.54 -0.85 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.995 r_dihedral_angle_3_deg 12.793 r_dihedral_angle_4_deg 11.428 r_dihedral_angle_1_deg 5.505 r_scangle_it 3.603 r_scbond_it 3.111 r_mcangle_it 1.621 r_angle_refined_deg 1.198 r_mcbond_it 1.074 r_nbtor_refined 0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.995 r_dihedral_angle_3_deg 12.793 r_dihedral_angle_4_deg 11.428 r_dihedral_angle_1_deg 5.505 r_scangle_it 3.603 r_scbond_it 3.111 r_mcangle_it 1.621 r_angle_refined_deg 1.198 r_mcbond_it 1.074 r_nbtor_refined 0.312 r_symmetry_vdw_refined 0.218 r_nbd_refined 0.209 r_xyhbond_nbd_refined 0.127 r_symmetry_hbond_refined 0.107 r_chiral_restr 0.082 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 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 r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2579 Nucleic Acid Atoms Solvent Atoms 296 Heterogen Atoms
Software Software Software Name Purpose d*TREK data scaling REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection CrystalClear data reduction CrystalClear data scaling