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Crystal structure of Peptidase M28 precursor (YP_926796.1) from SHEWANELLA AMAZONENSIS SB2B at 1.70 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 277 0.2000M MgCl2, 30.0000% PEG-400, 0.1M TRIS pH 8.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.91 57.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.442 α = 90 b = 84.867 β = 115.85 c = 80.114 γ = 90
Symmetry Space Group C 1 2 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) 2009-04-17 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.91837,0.97791 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 1.7 29.374 97.4 0.12 0.12 7.9 2.6 58230 10.978
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 1.7 1.74 96 0.462 0.462 1.9 2.6 4239
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 1.7 29.374 58229 2960 97.26 0.152 0.151 0.1606 0.182 0.1913 RANDOM 11.122
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] 0.06 -0.34 -0.17 -0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.001 r_dihedral_angle_4_deg 19.14 r_dihedral_angle_3_deg 11.636 r_dihedral_angle_1_deg 6.448 r_scangle_it 6.271 r_scbond_it 4.048 r_mcangle_it 2.466 r_mcbond_it 1.64 r_angle_refined_deg 1.471 r_angle_other_deg 0.909
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.001 r_dihedral_angle_4_deg 19.14 r_dihedral_angle_3_deg 11.636 r_dihedral_angle_1_deg 6.448 r_scangle_it 6.271 r_scbond_it 4.048 r_mcangle_it 2.466 r_mcbond_it 1.64 r_angle_refined_deg 1.471 r_angle_other_deg 0.909 r_mcbond_other 0.53 r_chiral_restr 0.087 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3283 Nucleic Acid Atoms Solvent Atoms 631 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building SCALA data scaling PDB_EXTRACT data extraction MOSFLM data reduction SHARP phasing