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Crystal structure of an alpha/beta hydrolase (YP_496220.1) from Novosphingobium aromaticivorans DSM 12444 at 1.50 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.1 277 NANODROP, 0.2M CaCl2, 20.0% PEG 3350, No Buffer pH 5.1, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2 38.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.48 α = 90 b = 69.95 β = 90 c = 82.22 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 325 mm CCD Flat mirror (vertical focusing) 2007-11-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.97908 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 1.5 27.714 98.8 0.105 7.8 41517 -3 11.671
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 1.5 1.55 97.4 0.704 1.5
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 SAD THROUGHOUT 1.5 27.714 41469 2095 99.07 0.163 0.161 0.168 0.203 0.2074 RANDOM 11.006
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] -0.4 0.46 -0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.231 r_dihedral_angle_4_deg 18.191 r_dihedral_angle_3_deg 12.551 r_dihedral_angle_1_deg 5.775 r_scangle_it 5.445 r_scbond_it 4.065 r_mcangle_it 2.605 r_mcbond_it 2.061 r_angle_refined_deg 1.671 r_angle_other_deg 1.041
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.231 r_dihedral_angle_4_deg 18.191 r_dihedral_angle_3_deg 12.551 r_dihedral_angle_1_deg 5.775 r_scangle_it 5.445 r_scbond_it 4.065 r_mcangle_it 2.605 r_mcbond_it 2.061 r_angle_refined_deg 1.671 r_angle_other_deg 1.041 r_mcbond_other 0.526 r_symmetry_vdw_other 0.28 r_symmetry_vdw_refined 0.24 r_nbd_refined 0.221 r_nbd_other 0.211 r_symmetry_hbond_refined 0.204 r_nbtor_refined 0.178 r_xyhbond_nbd_refined 0.166 r_chiral_restr 0.096 r_metal_ion_refined 0.091 r_nbtor_other 0.087 r_symmetry_metal_ion_refined 0.02 r_bond_refined_d 0.016 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 2185 Nucleic Acid Atoms Solvent Atoms 336 Heterogen Atoms 60
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