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E. coli PBP1b in complex with acyl-cephalexin and moenomycin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3VMA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 Drops contained 1uL of protein solution (20mg/mL protein, 100uM moenomycin and 2mM cephalexin) mixed with an equal volume of precipitant (20% w/v PEG 3350, 0.2M potassium/sodium tartate, 0.1M Bis Tris pH 8.5).
Crystal Properties Matthews coefficient Solvent content 3.57 65.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.7 α = 90 b = 63.76 β = 90 c = 297.62 γ = 90
Symmetry Space Group P 2 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 RAYONIX MX300HE 2013-02-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 1.00 CLSI 08ID-1
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 2.36 63.76 98.7 0.09 13.2 4.7 49407 42.47
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 2.36 2.42 0.65
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 3VMA 2.36 62.35 49337 2448 98.12 0.2388 0.2383 0.2566 0.2475 0.2674 RANDOM 60.79
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] 6.5139 13.6622 -20.1761
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 21.11 t_omega_torsion 2.17 t_angle_deg 1.11 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 21.11 t_omega_torsion 2.17 t_angle_deg 1.11 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 5466 Nucleic Acid Atoms Solvent Atoms 221 Heterogen Atoms 95
Software Software Software Name Purpose BUSTER refinement xia2 data reduction Aimless data scaling PHASER phasing