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Crystal structure of a ph domain containing bacterial protein (exig_2160) from exiguobacterium sibiricum 255-15 at 2.42 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9 277 NANODROP, 10.0% PEG 6000, 0.1M Bicine pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.07 59.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 150.99 α = 90 b = 150.99 β = 90 c = 76.219 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 ADSC QUANTUM 315 2007-08-31 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 0.9799, 0.9795, 1.0000 ALS 8.2.2
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 2.42 47.727 99.7 0.081 11.02 3.71 65515 -3 51.34
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 2.42 2.51 99.9 0.787 1.9 3.74
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 2.42 47.727 65460 3326 99.66 0.216 0.214 0.2193 0.254 0.2567 RANDOM 54.869
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] -3.16 -3.16 6.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.51 r_dihedral_angle_4_deg 15.324 r_dihedral_angle_3_deg 14.383 r_dihedral_angle_1_deg 4.608 r_scangle_it 3.324 r_mcangle_it 2.631 r_scbond_it 2.33 r_mcbond_it 1.684 r_angle_refined_deg 1.498 r_angle_other_deg 0.901
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.51 r_dihedral_angle_4_deg 15.324 r_dihedral_angle_3_deg 14.383 r_dihedral_angle_1_deg 4.608 r_scangle_it 3.324 r_mcangle_it 2.631 r_scbond_it 2.33 r_mcbond_it 1.684 r_angle_refined_deg 1.498 r_angle_other_deg 0.901 r_mcbond_other 0.46 r_nbd_refined 0.229 r_symmetry_vdw_refined 0.203 r_nbtor_refined 0.191 r_symmetry_vdw_other 0.182 r_nbd_other 0.181 r_xyhbond_nbd_refined 0.134 r_symmetry_hbond_refined 0.108 r_nbtor_other 0.087 r_chiral_restr 0.084 r_bond_refined_d 0.015 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8975 Nucleic Acid Atoms Solvent Atoms 173 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building XSCALE data scaling PDB_EXTRACT data extraction ADSC data collection XDS data reduction SHELXD phasing autoSHARP phasing