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Crystal structure of human pancreatic secretory protein ZG16p with O-(alpha-D-mannosyl)-L-threonine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3APA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.6 293 0.09M MES(pH 6.5), 0.09M Sodium phosphate, 0.09M Potassium phosphate, 1.8M Sodium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.09 41.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.397 α = 90 b = 73.022 β = 90 c = 30.4 γ = 90
Symmetry Space Group P 21 21 2
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 2011-02-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A Photon Factory BL-5A
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 2.7 50 98.3 0.1 17.5 6.8 3909
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 2.7 2.75 100 0.345 4.8 6.6
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 3APA 2.7 45.6 3660 170 98.6 0.22 0.217 0.2123 0.288 0.2751 RANDOM 27.43
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] -1.11 -0.9 2.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.411 r_dihedral_angle_4_deg 14.706 r_dihedral_angle_3_deg 12.956 r_dihedral_angle_1_deg 4.632 r_angle_refined_deg 0.827 r_scangle_it 0.392 r_nbtor_refined 0.296 r_mcangle_it 0.238 r_scbond_it 0.221 r_nbd_refined 0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.411 r_dihedral_angle_4_deg 14.706 r_dihedral_angle_3_deg 12.956 r_dihedral_angle_1_deg 4.632 r_angle_refined_deg 0.827 r_scangle_it 0.392 r_nbtor_refined 0.296 r_mcangle_it 0.238 r_scbond_it 0.221 r_nbd_refined 0.14 r_mcbond_it 0.129 r_symmetry_vdw_refined 0.094 r_xyhbond_nbd_refined 0.081 r_chiral_restr 0.047 r_symmetry_hbond_refined 0.04 r_bond_refined_d 0.005 r_gen_planes_refined 0.002 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 1084 Nucleic Acid Atoms Solvent Atoms 51 Heterogen Atoms 21
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement DENZO data reduction SCALA data scaling