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Crystal Structure of Heparinase II
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 5 293 17% PEG 3350, 0.2M sodium phosphate , pH 5.0, VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.47 50.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.046 α = 90 b = 119.339 β = 90 c = 200.7 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 100 CCD ADSC QUANTUM 315 2004-04-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 0.97910 NSLS X25
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.15 50 98.6 0.075 0.051 30.54 7.3 112668 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.15 2.25 98.4 0.226 0.145 10.1 7.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) 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 SAD THROUGHOUT 2.15 102.6 86490 86490 4640 98.73 0.19679 0.19478 0.1946 0.23456 0.2318 RANDOM 29.634
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] -1.75 5.56 -3.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.85 r_dihedral_angle_4_deg 16.709 r_dihedral_angle_3_deg 13.532 r_dihedral_angle_1_deg 5.93 r_scangle_it 1.426 r_angle_refined_deg 1.134 r_scbond_it 0.95 r_mcangle_it 0.577 r_mcbond_it 0.337 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.85 r_dihedral_angle_4_deg 16.709 r_dihedral_angle_3_deg 13.532 r_dihedral_angle_1_deg 5.93 r_scangle_it 1.426 r_angle_refined_deg 1.134 r_scbond_it 0.95 r_mcangle_it 0.577 r_mcbond_it 0.337 r_nbtor_refined 0.306 r_symmetry_vdw_refined 0.19 r_nbd_refined 0.187 r_symmetry_hbond_refined 0.137 r_xyhbond_nbd_refined 0.124 r_chiral_restr 0.075 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11956 Nucleic Acid Atoms Solvent Atoms 928 Heterogen Atoms 103
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling SOLVE phasing