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Crystal structure of human pancreatic secretory protein ZG16p with methyl alpha-D-mannopyranoside
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 VAPOR DIFFUSION, SITTING DROP 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 41.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.192 α = 90 b = 73.045 β = 90 c = 30.46 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 1.00000 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 2.8 50 99.7 0.17 10.8 6.7 3500
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 2.8 2.85 100 0.516 4.1 6.8
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3APA 2.8 45.5 3315 150 99.48 0.22362 0.22069 0.28463 0.2845 RANDOM 30.077
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] -2.18 -1.17 3.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.084 r_dihedral_angle_4_deg 16.837 r_dihedral_angle_3_deg 16.178 r_dihedral_angle_1_deg 5.592 r_angle_refined_deg 0.89 r_scangle_it 0.801 r_scbond_it 0.47 r_mcangle_it 0.429 r_nbtor_refined 0.305 r_mcbond_it 0.234
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.084 r_dihedral_angle_4_deg 16.837 r_dihedral_angle_3_deg 16.178 r_dihedral_angle_1_deg 5.592 r_angle_refined_deg 0.89 r_scangle_it 0.801 r_scbond_it 0.47 r_mcangle_it 0.429 r_nbtor_refined 0.305 r_mcbond_it 0.234 r_nbd_refined 0.167 r_symmetry_hbond_refined 0.146 r_symmetry_vdw_refined 0.138 r_xyhbond_nbd_refined 0.098 r_chiral_restr 0.051 r_bond_refined_d 0.006 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 32 Heterogen Atoms 15
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement DENZO data reduction SCALA data scaling