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Crystal structure of putative HAD superfamily hydrolase from Streptococcus agalactiae.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 298 0.1 M Bis-Tris pH 6.5, 25% PEG3350, 0.2 M Ammonium Acetate, Vapor diffusion, Sitting drop, temperature 298K, VAPOR DIFFUSION, SITTING DROP
Crystal Properties Matthews coefficient Solvent content 2.92 57.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.367 α = 90 b = 82.954 β = 90 c = 99.604 γ = 90
Symmetry Space Group I 2 2 2
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 ADSC QUANTUM 315 2008-08-15 SAD 2 1 x-ray CCD ADSC QUANTUM 4 2008-08-15 M SAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 0.979 NSLS X29A 2 SYNCHROTRON NSLS BEAMLINE X12C 0.979 NSLS X12C
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 1.55 50 97.1 0.103 0.082 29.6 10.5 48500 48500
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 1.55 1.61 91.4 0.645 0.553 2.64 4.2 4530
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 THROUGHOUT 1.55 50 48286 2443 96.59 0.18 0.179 0.1758 0.209 0.206 RANDOM 21.473
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] 0.58 0.6 -1.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.85 r_dihedral_angle_4_deg 19.638 r_dihedral_angle_3_deg 11.792 r_dihedral_angle_1_deg 5.939 r_scangle_it 3.801 r_scbond_it 2.428 r_mcangle_it 1.565 r_angle_refined_deg 1.561 r_mcbond_it 0.919 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.85 r_dihedral_angle_4_deg 19.638 r_dihedral_angle_3_deg 11.792 r_dihedral_angle_1_deg 5.939 r_scangle_it 3.801 r_scbond_it 2.428 r_mcangle_it 1.565 r_angle_refined_deg 1.561 r_mcbond_it 0.919 r_nbtor_refined 0.31 r_nbd_refined 0.208 r_symmetry_vdw_refined 0.173 r_symmetry_hbond_refined 0.129 r_metal_ion_refined 0.128 r_xyhbond_nbd_refined 0.11 r_chiral_restr 0.102 r_bond_refined_d 0.016 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2002 Nucleic Acid Atoms Solvent Atoms 282 Heterogen Atoms 7
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction CBASS data collection HKL-2000 data reduction SHELXE model building SHELXD phasing