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Crystal structure of heparin lyase I from Bacteroides thetaiotaomicron
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293 0.1M Na citrate pH 5.5, 2.0M Ammonium sulfate, vapor diffusion, hanging drop, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.76 55.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.921 α = 90 b = 68.712 β = 105.9 c = 61.306 γ = 90
Symmetry Space Group C 1 2 1
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 ADSC QUANTUM 210 2006-12-18 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD Bruker AXIOM 200 2007-03-28 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 4A 1.0000 PAL/PLS 4A 2 SYNCHROTRON PAL/PLS BEAMLINE 6B 0.97905, 0.97924, 0.97136 PAL/PLS 6B
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 1.8 58.93 92.2 0.057 21.3 4.4 43830 40417
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) 1.8 1.86 55.3 0.178 3.2 2415
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MAD THROUGHOUT 1.81 36.06 40417 2052 94.32 0.181 0.179 0.1701 0.216 0.2018 RANDOM 27.651
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] 2.36 0.51 -1.33 -0.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.437 r_dihedral_angle_4_deg 20.771 r_dihedral_angle_3_deg 15.722 r_dihedral_angle_1_deg 7.091 r_scangle_it 5.21 r_scbond_it 3.336 r_mcangle_it 2.297 r_angle_refined_deg 2.087 r_mcbond_it 1.402 r_chiral_restr 0.191
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.437 r_dihedral_angle_4_deg 20.771 r_dihedral_angle_3_deg 15.722 r_dihedral_angle_1_deg 7.091 r_scangle_it 5.21 r_scbond_it 3.336 r_mcangle_it 2.297 r_angle_refined_deg 2.087 r_mcbond_it 1.402 r_chiral_restr 0.191 r_bond_refined_d 0.027 r_gen_planes_refined 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2973 Nucleic Acid Atoms Solvent Atoms 259 Heterogen Atoms 31
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction