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The crystal structure of human Haloacid Dehalogenase-like Hydrolase Domain containing 1A (HDHD1A)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PIB 2PIB, 3HLT, 3K1Z, 2W4M experimental model PDB 3HLT 2PIB, 3HLT, 3K1Z, 2W4M experimental model PDB 3K1Z 2PIB, 3HLT, 3K1Z, 2W4M experimental model PDB 2W4M 2PIB, 3HLT, 3K1Z, 2W4M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277 0.1 M Sodium dihydrogen phosphate, 1.344 M di-potassium hydrogen phosphate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.86 68.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.19 α = 90 b = 85.19 β = 90 c = 103.03 γ = 120
Symmetry Space Group P 31 2 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 MARMOSAIC 225 mm CCD 2009-10-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.9795 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 42.59 99.5 0.107 0.107 9.4 4.1 29508
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 2.11 99 0.855 0.855 2 4.2 17548
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 2PIB, 3HLT, 3K1Z, 2W4M 2 42.6 28009 28009 1495 99.13 0.1677 0.1677 0.16542 0.1876 0.21272 0.2251 RANDOM 15.171
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] 0.81 0.4 0.81 -1.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.768 r_dihedral_angle_4_deg 24.654 r_dihedral_angle_3_deg 15.046 r_scangle_it 12.04 r_scbond_it 10.269 r_mcangle_it 6.212 r_dihedral_angle_1_deg 5.267 r_mcbond_it 4.763 r_mcbond_other 2.013 r_angle_refined_deg 1.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.768 r_dihedral_angle_4_deg 24.654 r_dihedral_angle_3_deg 15.046 r_scangle_it 12.04 r_scbond_it 10.269 r_mcangle_it 6.212 r_dihedral_angle_1_deg 5.267 r_mcbond_it 4.763 r_mcbond_other 2.013 r_angle_refined_deg 1.61 r_angle_other_deg 0.967 r_chiral_restr 0.098 r_bond_refined_d 0.018 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1835 Nucleic Acid Atoms Solvent Atoms 217 Heterogen Atoms 11
Software Software Software Name Purpose MAR345 data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling