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Crystal Structure of an archaeal aminopeptidase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VHE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 293 PEG 400, sodium chloride, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.6 51.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 158.34 α = 90 b = 158.34 β = 90 c = 114.46 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 CCD MARRESEARCH mirrors 2004-04-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 0.933 ESRF ID14-2
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 1.95 40 100 0.037 24.3 4.1 110425 110425 -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 1.95 2.07 63.5 0.193 5.2
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 1VHE 1.96 29.92 110402 107975 2427 100 0.18341 0.18341 0.18282 0.1827 0.2093 0.2082 RANDOM 37.662
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] 0.49 0.25 0.49 -0.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.093 r_dihedral_angle_4_deg 15.298 r_dihedral_angle_3_deg 14.228 r_dihedral_angle_1_deg 6.36 r_angle_refined_deg 1.316 r_scangle_it 0.966 r_scbond_it 0.568 r_mcangle_it 0.552 r_mcbond_it 0.367 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.093 r_dihedral_angle_4_deg 15.298 r_dihedral_angle_3_deg 14.228 r_dihedral_angle_1_deg 6.36 r_angle_refined_deg 1.316 r_scangle_it 0.966 r_scbond_it 0.568 r_mcangle_it 0.552 r_mcbond_it 0.367 r_nbtor_refined 0.303 r_symmetry_vdw_refined 0.205 r_nbd_refined 0.195 r_symmetry_hbond_refined 0.17 r_xyhbond_nbd_refined 0.12 r_chiral_restr 0.084 r_metal_ion_refined 0.027 r_bond_refined_d 0.009 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10514 Nucleic Acid Atoms Solvent Atoms 645 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction XDS data scaling MOLREP phasing