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Crystal structure of a putative metal dependent phosphohydrolase (sag1661) from streptococcus agalactiae serogroup v at 1.85 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6 277 NANODROP, 1.0M LiCl, 20.0% PEG-6000, 0.1M MES pH 6.0, VAPOR DIFFUSION,SITTING DROP, temperature 277K, VAPOR DIFFUSION, SITTING DROP, pH 6.00
Crystal Properties Matthews coefficient Solvent content 2.44 49.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.841 α = 90 b = 52.535 β = 114.29 c = 70.022 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) 2006-12-17 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.91837, 0.97935, 0.97864 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 1.85 40.555 99.6 0.073 11.13 37403 32.44
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 1.85 1.92 98.9 0.658 2
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 1.85 40.55 37389 1865 99.8 0.174 0.172 0.18 0.229 0.234 RANDOM 28.84
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] 1.6 -1.2 -0.27 -2.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.084 r_dihedral_angle_4_deg 19.576 r_dihedral_angle_3_deg 15.105 r_scangle_it 7.054 r_dihedral_angle_1_deg 5.734 r_scbond_it 5.18 r_mcangle_it 3.026 r_mcbond_it 2.051 r_angle_refined_deg 1.653 r_angle_other_deg 0.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.084 r_dihedral_angle_4_deg 19.576 r_dihedral_angle_3_deg 15.105 r_scangle_it 7.054 r_dihedral_angle_1_deg 5.734 r_scbond_it 5.18 r_mcangle_it 3.026 r_mcbond_it 2.051 r_angle_refined_deg 1.653 r_angle_other_deg 0.9 r_mcbond_other 0.632 r_symmetry_vdw_other 0.227 r_nbd_refined 0.222 r_nbtor_refined 0.191 r_xyhbond_nbd_refined 0.191 r_symmetry_hbond_refined 0.183 r_nbd_other 0.178 r_symmetry_vdw_refined 0.125 r_chiral_restr 0.094 r_nbtor_other 0.087 r_metal_ion_refined 0.049 r_bond_refined_d 0.018 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_xyhbond_nbd_other r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3089 Nucleic Acid Atoms Solvent Atoms 272 Heterogen Atoms 75
Software Software Software Name Purpose MolProbity model building SHELX phasing REFMAC refinement XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction SHELXD phasing autoSHARP phasing