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Crystal structure of Codakine at 1.3A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model Other HOMOLOGY MODEL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 0.2 M DI-AMMONIUM CITRATE PH 5, 20% W/V PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.1 41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.908 α = 90 b = 30.395 β = 133.86 c = 67.088 γ = 90
Symmetry Space Group C 1 2 1
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 CCD MIRRORS M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
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 1.3 33.11 89.7 0.03 12.1 3.3 26746 2 10.39
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 1.3 1.37 52.5 0.32 2.1 2.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 HOMOLOGY MODEL 1.3 27.63 2 26746 1370 89.2 0.145 0.144 0.161 0.1894 RANDOM 8.84
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] 0.943 0.552 -0.306 0.129
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.215 r_dihedral_angle_4_deg 16.083 r_dihedral_angle_3_deg 11.517 r_dihedral_angle_1_deg 6.361 r_scangle_it 3.518 r_scbond_it 2.421 r_angle_refined_deg 1.724 r_mcangle_it 1.664 r_mcbond_it 1.187 r_angle_other_deg 0.955
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.215 r_dihedral_angle_4_deg 16.083 r_dihedral_angle_3_deg 11.517 r_dihedral_angle_1_deg 6.361 r_scangle_it 3.518 r_scbond_it 2.421 r_angle_refined_deg 1.724 r_mcangle_it 1.664 r_mcbond_it 1.187 r_angle_other_deg 0.955 r_symmetry_vdw_refined 0.554 r_symmetry_vdw_other 0.36 r_nbd_refined 0.226 r_nbtor_refined 0.192 r_nbd_other 0.187 r_symmetry_hbond_refined 0.176 r_xyhbond_nbd_refined 0.137 r_chiral_restr 0.118 r_nbtor_other 0.089 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 992 Nucleic Acid Atoms Solvent Atoms 174 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling ACORN phasing