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X-ray crystal structure of the Py13 -pyrabactin complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3KLX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 1.7M (NH4)2SO4, 100mM cacodylate, 200mM NaCl, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.32 46.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.632 α = 90 b = 67.538 β = 90 c = 109.08 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 130 CCD MAR CCD 165 mm 2010-07-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BSRF BEAMLINE 3W1A 1.0 BSRF 3W1A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.83 50 91.6 35702 32704 3 5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.83 1.86 68.1 2.96 5.4 1194
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 3KLX 1.84 33.28 5 35702 32704 1731 97.81 0.20076 0.20076 0.19947 0.2182 0.224 0.2355 RANDOM 20.695
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] 0.07 -0.21 0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.17 r_dihedral_angle_4_deg 16.109 r_dihedral_angle_3_deg 13.946 r_dihedral_angle_1_deg 5.517 r_scangle_it 1.815 r_scbond_it 1.083 r_angle_refined_deg 1.066 r_mcangle_it 0.629 r_mcbond_it 0.337 r_chiral_restr 0.075
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.17 r_dihedral_angle_4_deg 16.109 r_dihedral_angle_3_deg 13.946 r_dihedral_angle_1_deg 5.517 r_scangle_it 1.815 r_scbond_it 1.083 r_angle_refined_deg 1.066 r_mcangle_it 0.629 r_mcbond_it 0.337 r_chiral_restr 0.075 r_bond_refined_d 0.008 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2841 Nucleic Acid Atoms Solvent Atoms 576 Heterogen Atoms 54
Software Software Software Name Purpose MAR345dtb data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling