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Tomato leucine aminopeptidase mutant - K354E
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4KSI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 0.1 M sodium cacodylate, pH 6.5, 0.35 M magnesium acetate, 10% PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.71 54.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.112 α = 90 b = 165.193 β = 90 c = 168.275 γ = 90
Symmetry Space Group C 2 2 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 IMAGE PLATE RIGAKU RAXIS IV++ 2011-05-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.541
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 2.15 33.92 100 0.108 0.043 15 7.3 96081 15.66
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.15 2.21 100 0.656 0.264 3 7.1 7061
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT 4KSI 2.15 30 94010 2000 99.93 0.1535 0.153 0.1619 0.1789 0.1858 RANDOM 30.968
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] 1.22 -0.35 -0.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.558 r_dihedral_angle_4_deg 15.335 r_dihedral_angle_3_deg 14.223 r_dihedral_angle_1_deg 6.266 r_mcangle_it 4.321 r_mcbond_it 2.748 r_mcbond_other 2.741 r_angle_refined_deg 1.329 r_angle_other_deg 0.956 r_chiral_restr 0.081
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.558 r_dihedral_angle_4_deg 15.335 r_dihedral_angle_3_deg 14.223 r_dihedral_angle_1_deg 6.266 r_mcangle_it 4.321 r_mcbond_it 2.748 r_mcbond_other 2.741 r_angle_refined_deg 1.329 r_angle_other_deg 0.956 r_chiral_restr 0.081 r_gen_planes_refined 0.017 r_gen_planes_other 0.008 r_bond_refined_d 0.007 r_bond_other_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11079 Nucleic Acid Atoms Solvent Atoms 1280 Heterogen Atoms 51
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing Coot model building PDB_EXTRACT data extraction