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Crystal structure of heparin lyase I complexed with disaccharide heparin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3IMN PDB ENTRY 3IMN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 22% glycerol, 20% PEG 1500, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.46 50.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.789 α = 90 b = 63.531 β = 115.47 c = 65.204 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 2007-12-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 4A 1.0000 PAL/PLS 4A
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 50 99 0.066 19.2 3.8 28413 28121
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) 2 2.07 95.7 0.102 3.4 2706
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3IMN 2 31.77 28059 2789 99.3 0.183 0.1825 0.217 0.2164 RANDOM 27.791
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] -7.449 -6.533 6.523 0.926
RMS Deviations Key Refinement Restraint Deviation c_scangle_it 2.966 c_mcangle_it 2.028 c_scbond_it 1.971 c_angle_deg 1.504 c_mcbond_it 1.333 c_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2978 Nucleic Acid Atoms Solvent Atoms 303 Heterogen Atoms 71
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing CNS refinement PDB_EXTRACT data extraction