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Crystal structure of methionine aminopeptidase from Pyrococcus furiosus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1WKM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 298 0.1 M Sodium acetate, 2M NaCl, 5% glycerol
Crystal Properties Matthews coefficient Solvent content 4.9 74.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 133.658 α = 90 b = 133.658 β = 90 c = 62.52 γ = 120
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 MAR scanner 345 mm plate 2019-10-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU R-AXIS IV 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 3.2 25 97 0.073 0.086 0.045 10.8 3.5 10354
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 3.2 3.31 86 0.398 0.496 0.291 0.823 2.5
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 1WKM 3.2 24.45 9862 492 96.79 0.1646 0.1621 0.1653 0.2137 0.2123 RANDOM 77.141
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] 0.02 0.01 0.02 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.591 r_dihedral_angle_4_deg 21.936 r_dihedral_angle_3_deg 17.415 r_dihedral_angle_1_deg 9.328 r_angle_refined_deg 1.74 r_angle_other_deg 1.209 r_chiral_restr 0.073 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.591 r_dihedral_angle_4_deg 21.936 r_dihedral_angle_3_deg 17.415 r_dihedral_angle_1_deg 9.328 r_angle_refined_deg 1.74 r_angle_other_deg 1.209 r_chiral_restr 0.073 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2308 Nucleic Acid Atoms Solvent Atoms 14 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing PDB_EXTRACT data extraction