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Crystal structure of methionine aminopeptidase from Rickettsia prowazekii bound to methionine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3MR1 PDB ENTRY 3MR1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 289 0.2 M sodium sulfate, 0.1 M BisTris propane, 20% PEG 3350, 20% ethylene glycol as cryo-protectant, 25.2 mg/mL protein, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.33 47.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.37 α = 90 b = 67.55 β = 97.429 c = 80.89 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 2010-04-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.97946 ALS 5.0.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.7 20 97.9 0.049 21.52 4.8 58037 -3 19.463
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 1.7 1.74 82.3 0.185 5.9 3.9
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 (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3MR1 1.7 19.983 57977 2932 97.794 0.162 0.1597 0.1985 0.2024 RANDOM 14.205
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] 0.002 -0.002 0.001 -0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.829 r_dihedral_angle_3_deg 11.537 r_dihedral_angle_1_deg 6.408 r_lrange_it 5.233 r_lrange_other 5.061 r_scangle_it 3.583 r_scangle_other 3.582 r_scbond_it 2.324 r_scbond_other 2.323 r_mcangle_other 1.788
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.829 r_dihedral_angle_3_deg 11.537 r_dihedral_angle_1_deg 6.408 r_lrange_it 5.233 r_lrange_other 5.061 r_scangle_it 3.583 r_scangle_other 3.582 r_scbond_it 2.324 r_scbond_other 2.323 r_mcangle_other 1.788 r_mcangle_it 1.78 r_mcbond_it 1.169 r_mcbond_other 1.164 r_angle_refined_deg 1.141 r_angle_other_deg 0.443 r_nbd_refined 0.205 r_symmetry_nbd_other 0.172 r_nbtor_refined 0.172 r_symmetry_xyhbond_nbd_refined 0.139 r_xyhbond_nbd_refined 0.132 r_nbd_other 0.129 r_symmetry_nbd_refined 0.106 r_symmetry_nbtor_other 0.075 r_chiral_restr 0.061 r_symmetry_xyhbond_nbd_other 0.059 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4086 Nucleic Acid Atoms Solvent Atoms 726 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling PHASER phasing PDB_EXTRACT data extraction XDS data reduction