☰ Navigation Tabs
Crystal structure of human Naa50 in complex with a truncated cofactor derived inhibitor (compound 2)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6WF3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 286.15 Co-crystallization: Naa50 apo protein (14.3 mg/ml) was incubated with compound 2 in a 1:3 molar ratio on ice for 60 min. Reservoir solution containing 0.2 M ammonium sulfate and 30% (w/v) PEG 3K/4K was mixed 1:1 with protein:ligand complex
Crystal Properties Matthews coefficient Solvent content 2.17 43.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.937 α = 90 b = 52.339 β = 97.38 c = 64.123 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 93 PIXEL DECTRIS PILATUS3 S 6M 2017-04-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.0 APS 17-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 2.04 63.59 98.8 0.126 0.991 7.9 3.3 21247
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.04 2.15 98.6 0.723 0.667 3.3
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 FOURIER SYNTHESIS THROUGHOUT 6WF3 2.04 50.52 21219 1023 98.6 0.224 0.222 0.2361 0.274 0.2909 RANDOM 35.3
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] -16.7048 -6.558 5.5496 11.1552
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 19.13 t_omega_torsion 2.97 t_angle_deg 1.13 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 19.13 t_omega_torsion 2.97 t_angle_deg 1.13 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle 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 2621 Nucleic Acid Atoms Solvent Atoms 98 Heterogen Atoms 96
Software Software Software Name Purpose BUSTER refinement PDB_EXTRACT data extraction XDS data reduction autoPROC data scaling BUSTER phasing