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Crystal structure of Fic protein from Mycoplasma mycoides
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5NH2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 293 0.1 M MES, 22% PEG400
Crystal Properties Matthews coefficient Solvent content 3.84 67.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.6 α = 90 b = 120.6 β = 90 c = 165.4 γ = 120
Symmetry Space Group P 31 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 PIXEL DECTRIS EIGER X 16M 2022-03-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL10U2 0.9792 SSRF BL10U2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) 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 3.499 50 95.6 0.153 0.168 0.998 10.56 18.5 18055 122.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.5 3.71 88.7 0.921 0.966 0.793 1.62 11.6
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 MOLECULAR REPLACEMENT THROUGHOUT 3.5 44.19 16231 1787 99.63 0.22197 0.21373 0.2454 0.29713 0.3041 RANDOM 139.589
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] 2.41 1.2 2.41 -7.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.387 r_long_range_B_refined 22.4 r_long_range_B_other 22.399 r_dihedral_angle_3_deg 21.625 r_scangle_other 18.36 r_mcangle_other 17.956 r_mcangle_it 17.955 r_dihedral_angle_4_deg 17.256 r_mcbond_it 12.11 r_mcbond_other 12.106
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.387 r_long_range_B_refined 22.4 r_long_range_B_other 22.399 r_dihedral_angle_3_deg 21.625 r_scangle_other 18.36 r_mcangle_other 17.956 r_mcangle_it 17.955 r_dihedral_angle_4_deg 17.256 r_mcbond_it 12.11 r_mcbond_other 12.106 r_scbond_it 12.067 r_scbond_other 12.066 r_dihedral_angle_1_deg 8.552 r_angle_refined_deg 1.581 r_angle_other_deg 1.144 r_chiral_restr 0.06 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 r_bond_other_d 0.001 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 6017 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 40
Software Software Software Name Purpose autoPROC data reduction autoPROC data scaling PHASER phasing PHENIX refinement