☰ Navigation Tabs
Crystal structure of putative metal-dependent hydrolase (YP_805737.1) from Lactobacillus casei ATCC 334 at 1.40 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 277 NANODROP, 1.0M LiCl, 20.0% PEG 6000, 0.1M HEPES pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.78 55.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 142.17 α = 90 b = 142.17 β = 90 c = 142.17 γ = 90
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) 2007-07-01 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.91837, 0.97917, 0.97891 SSRL BL11-1
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 1.4 29.025 99.8 0.067 16.16 93379 -3 16.76
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 1.4 1.45 98.5 0.011 1.7
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 1.4 29.025 93378 4683 99.96 0.135 0.134 0.1434 0.162 0.1673 RANDOM 16.7
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.029 r_dihedral_angle_4_deg 16.994 r_dihedral_angle_3_deg 12.692 r_sphericity_free 8.803 r_scangle_it 5.901 r_dihedral_angle_1_deg 5.883 r_sphericity_bonded 4.868 r_scbond_it 4.594 r_mcangle_it 3.397 r_mcbond_it 2.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.029 r_dihedral_angle_4_deg 16.994 r_dihedral_angle_3_deg 12.692 r_sphericity_free 8.803 r_scangle_it 5.901 r_dihedral_angle_1_deg 5.883 r_sphericity_bonded 4.868 r_scbond_it 4.594 r_mcangle_it 3.397 r_mcbond_it 2.79 r_rigid_bond_restr 2.033 r_mcbond_other 1.954 r_angle_refined_deg 1.543 r_angle_other_deg 1.014 r_symmetry_vdw_other 0.327 r_symmetry_hbond_refined 0.263 r_nbd_refined 0.235 r_nbd_other 0.198 r_symmetry_vdw_refined 0.193 r_nbtor_refined 0.188 r_xyhbond_nbd_refined 0.166 r_chiral_restr 0.098 r_metal_ion_refined 0.091 r_nbtor_other 0.089 r_bond_refined_d 0.016 r_xyhbond_nbd_other 0.014 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3012 Nucleic Acid Atoms Solvent Atoms 492 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building XSCALE data scaling PDB_EXTRACT data extraction MAR345 data collection XDS data reduction SHELXD phasing autoSHARP phasing