☰ Navigation Tabs
Crystal structure of S.aureus PNPase catalytic domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3CDI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2M CaCl2, 0.1M HEPES, 28% (v/v) PEG 400, pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.78 55.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.699 α = 98.22 b = 93.773 β = 95.34 c = 130.242 γ = 120.01
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 S 6M 2015-09-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.97846 SSRF BL19U1
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 2.2 50 91.4 0.099 14.7 3.3 171703
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 2.2 2.24 76.2 0.389 2.5 2.9
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 3CDI 2.2 49.24 150967 7966 83.97 0.22416 0.22287 0.2231 0.24852 0.2427 RANDOM 53.563
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] -4.74 -1.93 2.3 -4.57 2.18 10.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.317 r_dihedral_angle_4_deg 21.27 r_dihedral_angle_3_deg 18.011 r_long_range_B_refined 8.722 r_long_range_B_other 8.722 r_dihedral_angle_1_deg 6.018 r_scangle_other 5.929 r_mcangle_it 5.123 r_mcangle_other 5.123 r_scbond_it 3.656
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.317 r_dihedral_angle_4_deg 21.27 r_dihedral_angle_3_deg 18.011 r_long_range_B_refined 8.722 r_long_range_B_other 8.722 r_dihedral_angle_1_deg 6.018 r_scangle_other 5.929 r_mcangle_it 5.123 r_mcangle_other 5.123 r_scbond_it 3.656 r_scbond_other 3.644 r_angle_other_deg 3.573 r_mcbond_it 3.251 r_mcbond_other 3.251 r_angle_refined_deg 1.47 r_chiral_restr 0.077 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_gen_planes_other 0.007 r_bond_other_d r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 23885 Nucleic Acid Atoms Solvent Atoms 242 Heterogen Atoms 132
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing