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Mycobacterium Tuberculosis Methionine aminopeptidase type 1c (C105N mutant).
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YJ3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 0.1M Hepes, 27% Peg3350, 3% Glycerol
Crystal Properties Matthews coefficient Solvent content 1.95 36.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.285 α = 90 b = 48.536 β = 95 c = 56.353 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 IMAGE PLATE RIGAKU RAXIS IV++ 2015-04-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.01 28.63 100 0.045 0.061 0.041 0.998 16.7 1.9 17832 24.46
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.01 2.08 99.8 0.21 0.283 0.187 0.908 1.8
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 1YJ3 2.01 28.63 16891 943 99.88 0.1617 0.1592 0.1701 0.2082 0.2198 RANDOM 26.349
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.823 r_dihedral_angle_4_deg 19.471 r_dihedral_angle_3_deg 15.677 r_dihedral_angle_1_deg 6.452 r_angle_refined_deg 1.874 r_angle_other_deg 1.079 r_chiral_restr 0.131 r_bond_refined_d 0.018 r_gen_planes_refined 0.008 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.823 r_dihedral_angle_4_deg 19.471 r_dihedral_angle_3_deg 15.677 r_dihedral_angle_1_deg 6.452 r_angle_refined_deg 1.874 r_angle_other_deg 1.079 r_chiral_restr 0.131 r_bond_refined_d 0.018 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2154 Nucleic Acid Atoms Solvent Atoms 149 Heterogen Atoms 4
Software Software Software Name Purpose DENZO data collection SCALEPACK data scaling MOLREP model building REFMAC refinement PDB_EXTRACT data extraction DENZO data reduction HKL-2000 phasing