☰ Navigation Tabs
Crystal structure of putative haloacid dehalogenase-like hydrolase (YP_001086940.1) from Clostridium difficile 630 at 2.10 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9.1 277 NANODROP, 0.20M Na2HPO4, 20.0% PEG 3350, No Buffer pH 9.1, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.49 50.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.232 α = 90 b = 55.737 β = 96.97 c = 116.778 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 CCD MARMOSAIC 325 mm CCD Flat mirror (vertical focusing) 2008-11-13 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.91162, 0.97882, 0.97828 SSRL BL11-1
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 2.1 29.828 99.9 0.108 0.108 10.4 3.7 36707 27.96
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 2.1 2.15 99.6 0.503 0.503 2.1 3.6 2704
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 2.1 29.828 36695 1833 99.79 0.19 0.188 0.1927 0.23 0.2331 RANDOM 33.703
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] 3.82 -0.31 -0.3 -3.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.348 r_dihedral_angle_3_deg 10.67 r_dihedral_angle_4_deg 10.421 r_dihedral_angle_1_deg 4.228 r_scangle_it 3.473 r_scbond_it 2.371 r_mcangle_it 1.837 r_angle_refined_deg 1.635 r_angle_other_deg 1.348 r_mcbond_it 0.986
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.348 r_dihedral_angle_3_deg 10.67 r_dihedral_angle_4_deg 10.421 r_dihedral_angle_1_deg 4.228 r_scangle_it 3.473 r_scbond_it 2.371 r_mcangle_it 1.837 r_angle_refined_deg 1.635 r_angle_other_deg 1.348 r_mcbond_it 0.986 r_mcbond_other 0.185 r_nbd_refined 0.162 r_metal_ion_refined 0.156 r_nbtor_refined 0.153 r_nbd_other 0.14 r_xyhbond_nbd_refined 0.108 r_symmetry_vdw_other 0.104 r_chiral_restr 0.092 r_symmetry_vdw_refined 0.081 r_symmetry_hbond_refined 0.075 r_nbtor_other 0.073 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4217 Nucleic Acid Atoms Solvent Atoms 359 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building SCALA data scaling PDB_EXTRACT data extraction MAR345 data collection MOSFLM data reduction SHELXD phasing autoSHARP phasing