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Human methionine aminopeptidase type 1b (F309L mutant) in complex with Ovalicin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GZ5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.2 298 0.1M Bistris pH-6.2, 19% PEG3350, 5% glycerol
Crystal Properties Matthews coefficient Solvent content 2.55 51.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.392 α = 90 b = 77.339 β = 87.95 c = 47.464 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++ 2017-03-19 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) 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 1.6 50 99.8 0.056 0.065 0.034 17.3 3.6 45241
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 1.6 1.66 98.1 0.427 0.514 0.28 0.844 3.3
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 2GZ5 1.6 31.24 43101 2110 99.56 0.1782 0.177 0.1887 0.2012 0.2124 RANDOM 25.987
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] 0.52 -0.7 -1.52 0.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.584 r_dihedral_angle_3_deg 14.97 r_dihedral_angle_4_deg 14.123 r_dihedral_angle_1_deg 6.681 r_angle_refined_deg 1.726 r_angle_other_deg 1.062 r_chiral_restr 0.096 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.584 r_dihedral_angle_3_deg 14.97 r_dihedral_angle_4_deg 14.123 r_dihedral_angle_1_deg 6.681 r_angle_refined_deg 1.726 r_angle_other_deg 1.062 r_chiral_restr 0.096 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2393 Nucleic Acid Atoms Solvent Atoms 205 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement HKL-3000 data collection DENZO data reduction SCALEPACK data scaling MOLREP phasing PDB_EXTRACT data extraction