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S. aureus MnaA-UDP co-structure
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1F6D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 295 30% v/v PEG 400 0.1M Li2SO4, 0.1M NaCacodylate pH 6.5, 4mM Na2UDP
Crystal Properties Matthews coefficient Solvent content 2.2 43.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.19 α = 90 b = 82.78 β = 90 c = 170.88 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 100 CCD MARMOSAIC 300 mm CCD 2014-04-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 1.0000 CLSI 08ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 1.91 170.88 100 0.039 0.017 1 25.1 6.1 60512 34.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.91 2.14 100 0.369 0.161 0.952 4.8 6.2 16962
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 THROUGHOUT 1F6D 1.91 74.5 60432 3062 99.76 0.2049 0.2037 0.2054 0.2274 0.2286 RANDOM 41.26
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] 3.8066 -10.0876 6.281
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.31 t_omega_torsion 3.52 t_angle_deg 1.04 t_bond_d 0.01 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 16.31 t_omega_torsion 3.52 t_angle_deg 1.04 t_bond_d 0.01 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 5843 Nucleic Acid Atoms Solvent Atoms 187 Heterogen Atoms 99
Software Software Software Name Purpose BUSTER refinement Aimless data scaling MOLREP phasing PDB_EXTRACT data extraction PHENIX model building XDS data reduction