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Crystal structure of Putative cell invasion protein with MAC/Perforin domain (NP_812351.1) from BACTERIODES THETAIOTAOMICRON VPI-5482 at 2.46 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.7 277 5.0000% 2-methyl-2,4-pentanediol, 12.0000% polyethylene glycol 6000, 0.1M HEPES pH 6.7, NANODROP', VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.78 55.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.4 α = 90 b = 127.2 β = 90 c = 138.25 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 2009-07-31 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.97908,0.91837,0.97922 SSRL BL9-2
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 2.46 49.386 97.3 0.123 0.123 10.6 6.9 49779 52.436
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 2.46 2.59 94.2 0.752 0.752 2.3 5.9 6903
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 2.46 49.386 49764 2514 97.25 0.211 0.209 0.252 0.2465 RANDOM 29.993
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] -0.53 -1.35 1.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.408 r_dihedral_angle_4_deg 17.802 r_dihedral_angle_3_deg 15.066 r_dihedral_angle_1_deg 5.542 r_scangle_it 2.677 r_scbond_it 1.677 r_angle_refined_deg 1.465 r_mcangle_it 1.092 r_angle_other_deg 0.914 r_mcbond_it 0.573
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.408 r_dihedral_angle_4_deg 17.802 r_dihedral_angle_3_deg 15.066 r_dihedral_angle_1_deg 5.542 r_scangle_it 2.677 r_scbond_it 1.677 r_angle_refined_deg 1.465 r_mcangle_it 1.092 r_angle_other_deg 0.914 r_mcbond_it 0.573 r_mcbond_other 0.104 r_chiral_restr 0.086 r_bond_refined_d 0.014 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 7998 Nucleic Acid Atoms Solvent Atoms 239 Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building SCALA data scaling PDB_EXTRACT data extraction XDS data reduction SHELXD phasing autoSHARP phasing