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Crystal structure of aminopeptidase PepT (NP_980509.1) from Bacillus cereus ATCC 10987 at 2.04 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 293 NANODROP, 10.0% Glycerol, 5.0% PEG 1000, 30.0% PEG 600, 0.1M MES pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.63 53.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 141.311 α = 90 b = 58.147 β = 91.75 c = 51.368 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 collimating mirror, toroid focusing mirror 2009-01-17 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.91162, 0.97959 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 2.04 29.463 98.3 0.07 26596 -3 25.025
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 2.04 2.11 96.2 0.556 1.7
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 2.04 29.463 26590 1340 99.47 0.171 0.169 0.1704 0.212 0.2089 RANDOM 26.603
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] -1.65 -1.28 2.59 -1.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.442 r_dihedral_angle_3_deg 10.344 r_dihedral_angle_4_deg 9.757 r_scangle_it 7.882 r_scbond_it 5.531 r_dihedral_angle_1_deg 4.046 r_mcangle_it 2.774 r_mcbond_it 1.765 r_angle_refined_deg 1.635 r_angle_other_deg 0.957
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.442 r_dihedral_angle_3_deg 10.344 r_dihedral_angle_4_deg 9.757 r_scangle_it 7.882 r_scbond_it 5.531 r_dihedral_angle_1_deg 4.046 r_mcangle_it 2.774 r_mcbond_it 1.765 r_angle_refined_deg 1.635 r_angle_other_deg 0.957 r_mcbond_other 0.513 r_chiral_restr 0.098 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2761 Nucleic Acid Atoms Solvent Atoms 214 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building XSCALE data scaling PDB_EXTRACT data extraction MAR345 data collection XDS data reduction SHELXD phasing autoSHARP phasing