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Structural Basis of Catalysis by Mononuclear Methionine Aminopeptidase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XNZ PDB Entry 1XNZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 291 15% PEG 20000, 0.1 M MES (pH 6.5) , VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 1.99 38.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.809 α = 90 b = 64.257 β = 108.09 c = 76.172 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 2005-09-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
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 14.965 99.8 0.077 0.077 9.5 3.6 30975
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) 2 2.11 100 0.254 0.254 3 3.5 4498
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1XNZ 2 14.965 31011 30958 1545 99.8 0.209 0.204 0.196 0.1978 0.241 0.1988 RANDOM 13.902
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] -0.145 -1.163 -0.896 1.041
RMS Deviations Key Refinement Restraint Deviation c_scangle_it 2.899 c_scbond_it 2.064 c_mcangle_it 1.546 c_angle_d 1.277 c_mcbond_it 1.136 c_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4062 Nucleic Acid Atoms Solvent Atoms 267 Heterogen Atoms 24
Software Software Software Name Purpose SCALA data scaling MOLREP phasing CNS refinement PDB_EXTRACT data extraction MOSFLM data reduction CCP4 data scaling