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Staphylococcus aureus monofunctional glycosyltransferase in complex with moenomycin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HZS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 295 SA MGT E100Q (10 MG/ML) WAS MIXED
WITH 1MM MOENOMYCIN AND 1MM MNCL2 AND INCUBATED ON ICE FOR ~3
HOURS. PRECIPITATED MATERIAL WAS REMOVED BY CENTRIFUGATION AT 16,
000XG FOR 5 MINUTES. THE MOENOMYCIN COMPLEX WAS CRYSTALLIZED BY HANGING DROP VAPOR DIFFUSION, MIXING THE PROTEIN 1:1 WITH A RESERVOIR SOLUTION CONTAINING 0.1M NA ACETATE PH 4.6, 0.2M NACL, 30% MPD AT 295 K.
Crystal Properties Matthews coefficient Solvent content 3.35 63.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.422 α = 90 b = 114.422 β = 90 c = 128.844 γ = 120
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 RIGAKU SATURN 944 RIGAKU VARIMAX HF OPTICS 2007-09-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E DW 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 23.12 99.9 0.173 13.6 3.9 45531 2 37.46
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.2 100 0.381 3.2 3.8
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 3HZS 2.1 23.12 19082 963 99.8 0.199 0.197 0.2018 0.237 0.2438 RANDOM 42.1
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] 0.9141 0.9141 -1.8282
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 19.19 t_omega_torsion 3.11 t_angle_deg 1.06 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 19.19 t_omega_torsion 3.11 t_angle_deg 1.06 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 1713 Nucleic Acid Atoms Solvent Atoms 158 Heterogen Atoms 216
Software Software Software Name Purpose BUSTER refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing