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Crystal structure of the D1596A mutant of an engineered VWF A2 domain (N1493C and C1670S)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3PPV PDB ENTRY 3PPV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.2 293 0.1M sodium citrate, 1.6M (NH4)2SO4, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.6 52.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.059 α = 90 b = 72.059 β = 90 c = 76.258 γ = 120
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 MX225HE 2009-05-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 1.0000 SSRF BL17U
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 1.9 50 98.9 0.056 25.5 4.1 17603
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 1.9 1.97 97.7 0.231 19.2 3.1
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 PDB ENTRY 3PPV 1.9 32.58 16707 890 99.06 0.20471 0.20356 0.2048 0.2263 0.1886 RANDOM 15.44
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] 0.27 0.14 0.27 -0.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.334 r_dihedral_angle_3_deg 13.381 r_dihedral_angle_4_deg 11.818 r_dihedral_angle_1_deg 5.349 r_scangle_it 1.788 r_scbond_it 1.355 r_rigid_bond_restr 1.196 r_angle_refined_deg 1.086 r_sphericity_free 0.903 r_mcangle_it 0.728
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.334 r_dihedral_angle_3_deg 13.381 r_dihedral_angle_4_deg 11.818 r_dihedral_angle_1_deg 5.349 r_scangle_it 1.788 r_scbond_it 1.355 r_rigid_bond_restr 1.196 r_angle_refined_deg 1.086 r_sphericity_free 0.903 r_mcangle_it 0.728 r_sphericity_bonded 0.72 r_mcbond_it 0.384 r_nbtor_refined 0.3 r_symmetry_vdw_refined 0.183 r_nbd_refined 0.179 r_symmetry_hbond_refined 0.159 r_xyhbond_nbd_refined 0.093 r_chiral_restr 0.071 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1438 Nucleic Acid Atoms Solvent Atoms 193 Heterogen Atoms 1
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing