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Crystal Structure of IphB from Comamonas testosteroni KF1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4NBU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2M Ammonium sulfate, 0.1M sodium cacodylate trihydrate pH 6.5, 30% PEG8000
Crystal Properties Matthews coefficient Solvent content 2.36 47.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.03 α = 90 b = 75.7 β = 101.897 c = 73.64 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 PIXEL DECTRIS PILATUS 6M 2021-09-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 1.0 ELETTRA 11.2C
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 1.51 72.06 99.9 0.99 16.3 2 71252
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 1.51 1.54 0.763
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 (All) 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 1.518 72.058 71252 3437 99.898 0.133 0.132 0.1324 0.1618 0.162 RANDOM 24.226
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] 0.432 -0.122 0.754 -1.043
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.982 r_dihedral_angle_3_deg 13.086 r_lrange_other 11.034 r_lrange_it 11.033 r_scangle_it 9.026 r_scangle_other 9.024 r_dihedral_angle_2_deg 7.536 r_dihedral_angle_1_deg 6.736 r_scbond_it 6.559 r_scbond_other 6.558
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.982 r_dihedral_angle_3_deg 13.086 r_lrange_other 11.034 r_lrange_it 11.033 r_scangle_it 9.026 r_scangle_other 9.024 r_dihedral_angle_2_deg 7.536 r_dihedral_angle_1_deg 6.736 r_scbond_it 6.559 r_scbond_other 6.558 r_mcangle_other 6.157 r_mcangle_it 6.156 r_mcbond_it 4.345 r_mcbond_other 4.335 r_rigid_bond_restr 4.167 r_angle_refined_deg 1.791 r_angle_other_deg 0.634 r_symmetry_nbd_refined 0.267 r_nbd_refined 0.222 r_symmetry_nbd_other 0.186 r_nbtor_refined 0.177 r_nbd_other 0.143 r_xyhbond_nbd_refined 0.138 r_chiral_restr 0.096 r_ncsr_local_group_1 0.088 r_symmetry_xyhbond_nbd_refined 0.086 r_symmetry_nbtor_other 0.081 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3467 Nucleic Acid Atoms Solvent Atoms 262 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement AutoProcess data reduction Aimless data scaling MOLREP phasing