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crystal structure of Csn-PD from Paenibacillus dendritiformis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2D05
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1M Citric acid pH3.5, 25% PEG3,350
Crystal Properties Matthews coefficient Solvent content 1.82 32.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.51 α = 90 b = 73.138 β = 90 c = 99.975 γ = 90
Symmetry Space Group C 2 2 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 PIXEL DECTRIS PILATUS3 6M 2021-08-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 1.18071 CLSI 08ID-1
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 1.68 44.72 99.4 0.052 21.7 6.6 28796
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 1.68 1.71 0.446
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 (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2d05 1.68 44.72 28766 1455 99.244 0.152 0.1497 0.1951 0.1887 21.494
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] 2.846 -1.079 -1.767
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.463 r_dihedral_angle_4_deg 17.218 r_dihedral_angle_3_deg 11.945 r_dihedral_angle_1_deg 5.718 r_lrange_it 5.576 r_lrange_other 5.496 r_scangle_it 4.6 r_scangle_other 4.598 r_scbond_it 3.022 r_scbond_other 3.021
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.463 r_dihedral_angle_4_deg 17.218 r_dihedral_angle_3_deg 11.945 r_dihedral_angle_1_deg 5.718 r_lrange_it 5.576 r_lrange_other 5.496 r_scangle_it 4.6 r_scangle_other 4.598 r_scbond_it 3.022 r_scbond_other 3.021 r_mcangle_other 2.27 r_mcangle_it 2.269 r_mcbond_it 1.656 r_angle_refined_deg 1.639 r_mcbond_other 1.63 r_angle_other_deg 1.557 r_symmetry_nbd_refined 0.242 r_nbd_refined 0.22 r_nbd_other 0.184 r_symmetry_nbd_other 0.181 r_nbtor_refined 0.179 r_symmetry_xyhbond_nbd_refined 0.176 r_xyhbond_nbd_refined 0.167 r_symmetry_xyhbond_nbd_other 0.116 r_chiral_restr 0.087 r_symmetry_nbtor_other 0.083 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2030 Nucleic Acid Atoms Solvent Atoms 238 Heterogen Atoms 17
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing