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Crystal structure of C105S mutant of Mycobacterium tuberculosis methionine aminopeptidase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Y1N PDB ENTRY 1Y1N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.8 298 PEG 2000, Bistris, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.09 41.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.22 α = 90 b = 48.66 β = 95.16 c = 55.72 γ = 90
Symmetry Space Group P 1 21 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 ADSC QUANTUM 315 2004-07-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 1.00 ALS 8.2.2
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 38.5 87.8 0.154 0.127 5.6 2.8 15726 15726 1 1 17.6
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 2.11 90.8 0.399 2.1 2.8 2364
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 PDB ENTRY 1Y1N 2 28.52 14906 798 87.66 0.2142 0.21088 0.2143 0.2737 0.2745 RANDOM 22.573
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] 0.01 0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.551 r_dihedral_angle_4_deg 20.989 r_dihedral_angle_3_deg 17.463 r_dihedral_angle_1_deg 7.134 r_scangle_it 4.326 r_scbond_it 2.833 r_angle_refined_deg 1.924 r_mcangle_it 1.609 r_mcbond_it 0.949 r_chiral_restr 0.122
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.551 r_dihedral_angle_4_deg 20.989 r_dihedral_angle_3_deg 17.463 r_dihedral_angle_1_deg 7.134 r_scangle_it 4.326 r_scbond_it 2.833 r_angle_refined_deg 1.924 r_mcangle_it 1.609 r_mcbond_it 0.949 r_chiral_restr 0.122 r_bond_refined_d 0.021 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2153 Nucleic Acid Atoms Solvent Atoms 56 Heterogen Atoms 7
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling