☰ Navigation Tabs
Aeropyrum pernix acylaminoacyl peptidase, H367A mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VE6 PDB ENTRY 1VE6 (ONE MONOMER)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.35 293 169 mM sodium acetate, 0.4 mM EDTA, 2% PEG 4000 0.51% beta-octyl-glucoside, pH 6.35, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.43 49.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.27 α = 90 b = 105.04 β = 90 c = 114.02 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 293 IMAGE PLATE RIGAKU RAXIS IIC 2006-02-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
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 2.2 20 93.2 0.118 11.5 3.71 58729 -3 38.14
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.5 93.6 0.467 0.467 3.61 3.42 18581
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 PDB ENTRY 1VE6 (ONE MONOMER) 2.2 19.69 55723 55723 2982 93.34 0.17959 0.17959 0.17739 0.1747 0.22225 0.221 RANDOM 35.778
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] 0.01 0.01 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.37 r_dihedral_angle_4_deg 21.238 r_dihedral_angle_3_deg 16.015 r_dihedral_angle_1_deg 6.954 r_scangle_it 3.067 r_mcangle_it 2.457 r_scbond_it 2.052 r_mcbond_it 1.592 r_angle_refined_deg 1.502 r_nbtor_refined 0.314
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.37 r_dihedral_angle_4_deg 21.238 r_dihedral_angle_3_deg 16.015 r_dihedral_angle_1_deg 6.954 r_scangle_it 3.067 r_mcangle_it 2.457 r_scbond_it 2.052 r_mcbond_it 1.592 r_angle_refined_deg 1.502 r_nbtor_refined 0.314 r_symmetry_hbond_refined 0.276 r_nbd_refined 0.212 r_xyhbond_nbd_refined 0.157 r_symmetry_vdw_refined 0.109 r_chiral_restr 0.091 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other 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 8657 Nucleic Acid Atoms Solvent Atoms 183 Heterogen Atoms
Software Software Software Name Purpose bioteX data collection MOLREP phasing REFMAC refinement XDS data reduction XSCALE data scaling