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Crystal structure of a apo form cyclase from Fischerella sp.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5YVK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 295 1.0M sodium citrate, 0.1M Imidazole pH 8.0
Crystal Properties Matthews coefficient Solvent content 5.01 75.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.993 α = 90 b = 90.993 β = 90 c = 234.496 γ = 90
Symmetry Space Group P 41 21 2
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 RAYONIX MX-300 2018-01-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL15A1 1.0 NSRRC BL15A1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.35 25 96.8 0.077 0.082 0.028 12.2 8.9 40767
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.35 2.43 100 0.706 0.745 0.231 0.856 10.1
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 5YVK 2.35 24.85 38471 1959 96.17 0.19692 0.19506 0.2179 0.2334 0.2475 RANDOM 54.156
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] -0.89 -0.89 1.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.126 r_dihedral_angle_4_deg 20.35 r_dihedral_angle_3_deg 18.328 r_long_range_B_other 10.256 r_long_range_B_refined 10.245 r_scangle_other 8.911 r_dihedral_angle_1_deg 7.983 r_scbond_it 6.644 r_scbond_other 6.642 r_mcangle_it 6.539
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.126 r_dihedral_angle_4_deg 20.35 r_dihedral_angle_3_deg 18.328 r_long_range_B_other 10.256 r_long_range_B_refined 10.245 r_scangle_other 8.911 r_dihedral_angle_1_deg 7.983 r_scbond_it 6.644 r_scbond_other 6.642 r_mcangle_it 6.539 r_mcangle_other 6.538 r_mcbond_it 5.073 r_mcbond_other 5.056 r_angle_refined_deg 1.38 r_angle_other_deg 0.86 r_chiral_restr 0.063 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 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 3088 Nucleic Acid Atoms Solvent Atoms 220 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PHASER phasing PDB_EXTRACT data extraction HKL-2000 data reduction