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Crystal structure of human pancreatic secretory protein ZG16b
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3APA PDB ENTRY 3APA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 0.4M ammonium phosphate monobasic, 5%(v/v) 1,4-dioxane, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.99 38.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.39 α = 90 b = 66.631 β = 90 c = 67.585 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 2010-05-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A 1.0000 Photon Factory AR-NE3A
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 2.75 50 99.9 0.164 14 10.3 7629 7619
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) 2.75 2.8 99.7 0.501 3.5 8.8 369
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3APA 2.75 40 7229 7229 345 99.62 0.223 0.22 0.2161 0.283 0.2745 RANDOM 26.8
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] 1.36 -1.96 0.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.766 r_dihedral_angle_3_deg 22.348 r_dihedral_angle_4_deg 15.365 r_dihedral_angle_1_deg 6.917 r_scangle_it 1.866 r_angle_refined_deg 1.496 r_scbond_it 1.209 r_mcangle_it 1.053 r_mcbond_it 0.593 r_nbtor_refined 0.316
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.766 r_dihedral_angle_3_deg 22.348 r_dihedral_angle_4_deg 15.365 r_dihedral_angle_1_deg 6.917 r_scangle_it 1.866 r_angle_refined_deg 1.496 r_scbond_it 1.209 r_mcangle_it 1.053 r_mcbond_it 0.593 r_nbtor_refined 0.316 r_nbd_refined 0.234 r_symmetry_hbond_refined 0.23 r_symmetry_vdw_refined 0.216 r_xyhbond_nbd_refined 0.168 r_chiral_restr 0.1 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 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 2132 Nucleic Acid Atoms Solvent Atoms 50 Heterogen Atoms 10
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling