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Crystal Structure of SilF (apo form)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VB2 2VB2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 0.01 M Zinc sulphate heptahydrate, 0.1 M MES pH 6.5, 25%
v/v PEG 550 MME
Crystal Properties Matthews coefficient Solvent content 1.91 35.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.47 α = 90 b = 109.47 β = 90 c = 84.59 γ = 120
Symmetry Space Group P 65 2 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 PIXEL DECTRIS PILATUS3 6M 2019-11-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.999 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.2 47.402 98.87 1 15.1 36.9 15531
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.279 0.6
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2VB2 2.2 47.402 15531 802 98.898 0.217 0.2147 0.2187 0.2596 0.2575 50.07
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] -0.013 -0.007 -0.013 0.043
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.225 r_dihedral_angle_4_deg 15.994 r_dihedral_angle_3_deg 14.123 r_lrange_other 11.553 r_lrange_it 11.552 r_scangle_it 9.083 r_scangle_other 9.079 r_dihedral_angle_1_deg 6.785 r_mcangle_it 6.079 r_mcangle_other 6.077
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.225 r_dihedral_angle_4_deg 15.994 r_dihedral_angle_3_deg 14.123 r_lrange_other 11.553 r_lrange_it 11.552 r_scangle_it 9.083 r_scangle_other 9.079 r_dihedral_angle_1_deg 6.785 r_mcangle_it 6.079 r_mcangle_other 6.077 r_scbond_it 6.01 r_scbond_other 6.007 r_mcbond_it 4.314 r_mcbond_other 4.313 r_angle_other_deg 2.336 r_angle_refined_deg 1.558 r_symmetry_nbd_refined 0.418 r_nbd_other 0.27 r_symmetry_metal_ion_refined 0.26 r_nbd_refined 0.214 r_symmetry_nbd_other 0.212 r_symmetry_xyhbond_nbd_refined 0.162 r_nbtor_refined 0.151 r_xyhbond_nbd_refined 0.149 r_xyhbond_nbd_other 0.088 r_symmetry_nbtor_other 0.075 r_chiral_restr 0.064 r_bond_other_d 0.035 r_bond_refined_d 0.01 r_gen_planes_other 0.009 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1782 Nucleic Acid Atoms Solvent Atoms 10 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing