☰ Navigation Tabs
Crystal structure of CBM20 domain of human putative glycerophosphodiester phosphodiesterase 5 (KIAA1434)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 293 1.0M Sodium/Potassium Phosphate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.26 62.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.04 α = 90 b = 111.04 β = 90 c = 77.385 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 RIGAKU JUPITER 210 rhodium coated mirror 2006-09-22 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B2 0.979270, 0.979740, 0.96400 SPring-8 BL26B2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 50 90.7 0.052 29.9 5.1 65368 10.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.03 50.4 0.287 3.8 3.8 1809
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MAD THROUGHOUT 2 50 62030 3302 90.73 0.222 0.221 0.2164 0.243 0.2171 RANDOM 16.625
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] 0.54 0.27 0.54 -0.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.833 r_dihedral_angle_4_deg 13.216 r_dihedral_angle_3_deg 11.578 r_dihedral_angle_1_deg 4.169 r_scangle_it 1.568 r_angle_refined_deg 1.233 r_scbond_it 1.049 r_mcangle_it 0.88 r_mcbond_it 0.552 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.833 r_dihedral_angle_4_deg 13.216 r_dihedral_angle_3_deg 11.578 r_dihedral_angle_1_deg 4.169 r_scangle_it 1.568 r_angle_refined_deg 1.233 r_scbond_it 1.049 r_mcangle_it 0.88 r_mcbond_it 0.552 r_nbtor_refined 0.303 r_symmetry_hbond_refined 0.193 r_nbd_refined 0.184 r_xyhbond_nbd_refined 0.181 r_symmetry_vdw_refined 0.174 r_chiral_restr 0.08 r_bond_refined_d 0.008 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 5132 Nucleic Acid Atoms Solvent Atoms 448 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement BSS data collection HKL-2000 data reduction HKL-2000 data scaling SOLVE phasing