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Structure of the central NEAT domain, N2, of the listerial Hbp2 protein, apo form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3SZ6 PDB ENTRY 3SZ6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 5.4 298 100 mM sodium citrate tribasic dihydrate, 200 mM potassium sodium tartrate tetrahydrate, 2.0 M ammonium sulfate, pH 5.4, vapor diffusion, temperature 298K, EVAPORATION
Crystal Properties Matthews coefficient Solvent content 2.19 43.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.3 α = 90 b = 89.3 β = 90 c = 89.3 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M MIRRORS. BENT CYLINDERS, STRIPES OF PT, RH AND CLEAR. 2013-06-06 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.97950, 0.9686, 1.5418 APS 24-ID-C
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 2.7 63.14 100 0.052 35.3 21.4 3370 -3 109.36
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 2.7 2.85 100 0.471 6.3 22.8
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT PDB ENTRY 3SZ6 2.7 63.14 5408 3370 337 100 0.258 0.254 0.2632 0.293 0.2903 RANDOM 120.65
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]
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 19.66 t_omega_torsion 1.79 t_angle_deg 1.02 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_other_torsion 19.66 t_omega_torsion 1.79 t_angle_deg 1.02 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 947 Nucleic Acid Atoms Solvent Atoms 9 Heterogen Atoms 5
Software Software Software Name Purpose SCALEPACK data scaling MLPHARE phasing DM phasing BUSTER-TNT refinement PDB_EXTRACT data extraction XSCALE data scaling BUSTER refinement