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Crystal Structure of Human Haloacid Dehalogenase-like Hydrolase Domain containing 3 (HDHD3)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 0.49M NaH2PO4, 0.91M K2HPO4, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.15 42.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.625 α = 90 b = 62.455 β = 90 c = 79.665 γ = 90
Symmetry Space Group P 21 21 21
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 MARMOSAIC 225 mm CCD 2009-09-07 M SAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.9773, 0.9796 Diamond I02
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 1.55 43.32 99.4 0.06 0.06 11.5 4.1 37908
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) 1 1.55 1.63 98.7 0.552 0.552 2 3.6 19357
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 SAD THROUGHOUT 1.55 43.32 35966 35966 1892 99.27 0.16935 0.16935 0.16744 0.1967 0.20688 0.2386 RANDOM 10.979
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] -0.44 0.06 0.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.749 r_dihedral_angle_4_deg 21.337 r_dihedral_angle_3_deg 11.842 r_scangle_it 8.284 r_scbond_it 5.83 r_dihedral_angle_1_deg 5.786 r_mcangle_it 3.873 r_mcbond_it 2.876 r_angle_refined_deg 1.443 r_mcbond_other 1.148
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.749 r_dihedral_angle_4_deg 21.337 r_dihedral_angle_3_deg 11.842 r_scangle_it 8.284 r_scbond_it 5.83 r_dihedral_angle_1_deg 5.786 r_mcangle_it 3.873 r_mcbond_it 2.876 r_angle_refined_deg 1.443 r_mcbond_other 1.148 r_angle_other_deg 0.943 r_chiral_restr 0.081 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1895 Nucleic Acid Atoms Solvent Atoms 303 Heterogen Atoms 10
Software Software Software Name Purpose MAR345 data collection SHELXCD phasing REFMAC refinement MOSFLM data reduction SCALA data scaling