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The crystal structure of human haloacid dehalogenase-like hydrolase domain containing 2 (HDHD2)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HO4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 2.6 M Ammonium sulphate, 1% MPD, 0.1M HEPES pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.36 47.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.94 α = 90 b = 77.68 β = 90 c = 103.99 γ = 90
Symmetry Space Group P 21 2 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 2009-05-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.97240 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 2.3 28.36 99.6 0.063 0.063 10.4 3.4 25410
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 2.3 2.42 99.9 0.804 0.804 1.5 3.5 12741
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT 2HO4 2.3 28.36 21115 24115 1264 99.45 0.21598 0.21598 0.21346 0.2204 0.2658 0.2728 RANDOM 23.195
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] -0.27 -1.33 1.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.488 r_dihedral_angle_3_deg 16.011 r_dihedral_angle_4_deg 15.677 r_dihedral_angle_1_deg 5.963 r_scangle_it 2.723 r_scbond_it 1.784 r_angle_refined_deg 1.422 r_mcangle_it 0.871 r_mcbond_it 0.48 r_chiral_restr 0.087
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.488 r_dihedral_angle_3_deg 16.011 r_dihedral_angle_4_deg 15.677 r_dihedral_angle_1_deg 5.963 r_scangle_it 2.723 r_scbond_it 1.784 r_angle_refined_deg 1.422 r_mcangle_it 0.871 r_mcbond_it 0.48 r_chiral_restr 0.087 r_bond_refined_d 0.013 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3630 Nucleic Acid Atoms Solvent Atoms 64 Heterogen Atoms 14
Software Software Software Name Purpose MAR345 data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling