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Crystal structure of methionine aminopeptidase from Rickettsia prowazekii
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, SITTING DROP 8 289 0.1 M SPG buffer pH 8.0, 25% PEG 1500 with 20% ethylene glycol as cryoprotectant, 29 mg/mL protein, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.53 51.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.48 α = 90 b = 114.85 β = 92.66 c = 115.8 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 2010-04-23 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 2 42.4 98.1 0.08 15.32 4.91 73427 -3
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 2 2.05 84 0.26 4.6 3.63
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 PDB ENTRY 1xnz 2 42.4 69661 3700 98.01 0.17271 0.17056 0.1734 0.21229 0.1776 RANDOM 15.352
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] -0.04 -0.13 -1.12 1.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.865 r_dihedral_angle_4_deg 23.233 r_dihedral_angle_3_deg 13.119 r_dihedral_angle_1_deg 6.233 r_scangle_it 3.247 r_scbond_it 2.034 r_angle_refined_deg 1.41 r_mcangle_it 1.108 r_mcbond_it 0.631 r_chiral_restr 0.101
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.865 r_dihedral_angle_4_deg 23.233 r_dihedral_angle_3_deg 13.119 r_dihedral_angle_1_deg 6.233 r_scangle_it 3.247 r_scbond_it 2.034 r_angle_refined_deg 1.41 r_mcangle_it 1.108 r_mcbond_it 0.631 r_chiral_restr 0.101 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7691 Nucleic Acid Atoms Solvent Atoms 1073 Heterogen Atoms 34
Software Software Software Name Purpose XSCALE data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction