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Crystal structure of aminopeptidase from marine sediment archaeon Thaumarchaeota archaeon
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MPX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277 0.2 M Na citrate, 20% PEG3350, 2.8 mM DL-Phe
Crystal Properties Matthews coefficient Solvent content 2.69 54.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.434 α = 90 b = 108.144 β = 95.08 c = 120.384 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 315r mirrors 2013-10-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.979268 APS 19-ID
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 2.1 30 99.8 0.137 9 3.2 176913 176530 -3 24.97
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 2.1 2.14 99.8 0.57 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 FREE R-VALUE 1MPX 2.1 29.69 175745 2166 99.77 0.2054 0.2051 0.2214 0.2288 0.2477 RANDOM 24.45
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] -0.3675 -2.0413 2.7541 -2.3865
RMS Deviations Key Refinement Restraint Deviation t_omega_torsion 3.26 t_other_torsion 2.8 t_angle_deg 0.73 t_bond_d 0.008 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_omega_torsion 3.26 t_other_torsion 2.8 t_angle_deg 0.73 t_bond_d 0.008 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 19666 Nucleic Acid Atoms Solvent Atoms 1124 Heterogen Atoms 1254
Software Software Software Name Purpose BUSTER refinement SBC-Collect data collection HKL-3000 data scaling MOLREP phasing