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Crystal structure of pleckstrin homology domain (YP_926556.1) from SHEWANELLA AMAZONENSIS SB2B at 1.99 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 5.0000% polyethylene glycol 3000, 22.0000% polyethylene glycol 400, 10.0000% Glycerol, 0.1M HEPES pH 7.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K, VAPOR DIFFUSION, SITTING DROP
Crystal Properties Matthews coefficient Solvent content 2.07 40.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.23 α = 90 b = 129.49 β = 90 c = 138.73 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 collimating mirror, toroid focusing mirror 2009-05-14 M MAD 2 1 x-ray 100 CCD MARMOSAIC 325 mm CCD Flat collimating mirror, toroid focusing mirror 2009-05-14 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.97920 SSRL BL9-2 2 SYNCHROTRON SSRL BEAMLINE BL9-2 0.97920,0.97934,0.91837 SSRL BL9-2
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 1,2 1.99 47.351 98.4 0.087 10.18 3.61 41702 -3 22.653
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) 1,2 1.99 2.06 99.1 0.531 2.3
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 1.99 47.351 41641 2115 98.47 0.191 0.189 0.1934 0.233 0.2389 RANDOM 22.491
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] 1.33 -0.51 -0.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.871 r_dihedral_angle_4_deg 19.476 r_dihedral_angle_3_deg 13.43 r_dihedral_angle_1_deg 5.294 r_scangle_it 4.304 r_scbond_it 2.684 r_mcangle_it 2.454 r_angle_refined_deg 1.664 r_mcbond_it 1.403 r_angle_other_deg 0.981
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.871 r_dihedral_angle_4_deg 19.476 r_dihedral_angle_3_deg 13.43 r_dihedral_angle_1_deg 5.294 r_scangle_it 4.304 r_scbond_it 2.684 r_mcangle_it 2.454 r_angle_refined_deg 1.664 r_mcbond_it 1.403 r_angle_other_deg 0.981 r_mcbond_other 0.323 r_chiral_restr 0.099 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4634 Nucleic Acid Atoms Solvent Atoms 242 Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction SHELXD phasing autoSHARP phasing