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Crystal structure of a protein of uknown function (NP_471338.1) from Listeria innocua at 1.74 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP, NANODROP 4.6 277 30.0% Glycerol, 5.6% PEG-4000, 0.1M Acetate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K 2 VAPOR DIFFUSION, SITTING DROP, NANODROP 4.5 277 0.2M Ca(OAc)2, 30.0% PEG-400, 0.1M Acetate, pH 4.5, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.11 α = 90 b = 100.11 β = 90 c = 66.916 γ = 120
Symmetry Space Group P 63 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 Flat mirror (vertical focusing) 2006-07-17 M MAD 2 2
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 1.000001 SSRL BL11-1 2 SYNCHROTRON SSRL BEAMLINE BL11-1 0.979291, 0.918370, 0.978981 SSRL BL11-1
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 1.74 29.424 98.7 0.076 0.076 6.4 11.5 20444
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 1.74 1.79 96.8 0.852 0.852 0.9 7.1 1376
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 1.74 29.424 20422 1072 97.43 0.175 0.173 0.1839 0.207 0.2204 RANDOM 28.343
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] 1.02 0.51 1.02 -1.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.756 r_dihedral_angle_3_deg 12.542 r_dihedral_angle_4_deg 10.064 r_scangle_it 6.869 r_scbond_it 4.825 r_dihedral_angle_1_deg 4.054 r_mcangle_it 2.738 r_mcbond_it 2.111 r_angle_refined_deg 1.211 r_angle_other_deg 0.797
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.756 r_dihedral_angle_3_deg 12.542 r_dihedral_angle_4_deg 10.064 r_scangle_it 6.869 r_scbond_it 4.825 r_dihedral_angle_1_deg 4.054 r_mcangle_it 2.738 r_mcbond_it 2.111 r_angle_refined_deg 1.211 r_angle_other_deg 0.797 r_mcbond_other 0.494 r_nbd_refined 0.233 r_nbtor_refined 0.192 r_symmetry_vdw_refined 0.191 r_symmetry_hbond_refined 0.17 r_xyhbond_nbd_refined 0.162 r_nbd_other 0.16 r_symmetry_vdw_other 0.143 r_nbtor_other 0.082 r_chiral_restr 0.079 r_bond_refined_d 0.018 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1044 Nucleic Acid Atoms Solvent Atoms 97 Heterogen Atoms
Software Software Software Name Purpose MolProbity model building SHELX phasing REFMAC refinement SCALA data scaling PDB_EXTRACT data extraction MOSFLM data reduction CCP4 data scaling SHELXD phasing autoSHARP phasing