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Crystal Structure of IphB from Comamonas testosteroni KF1 in complex with NADP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 25RT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 4M Ammonium acetate, 0.1 M Sodium acetate trihydrate pH 4.6
Crystal Properties Matthews coefficient Solvent content 2.2 43.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.84 α = 90 b = 152.281 β = 90 c = 74.177 γ = 90
Symmetry Space Group C 2 2 21
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 RIGAKU HyPix-6000HE 2021-12-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54
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 1.8 28.011 100 0.999 18.5 7.1 41740
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 1.8 1.84 0.902
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 1.8 28.011 41718 2052 99.933 0.138 0.1358 0.1359 0.1771 0.1769 RANDOM 17.304
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] -1.001 0.115 0.886
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.233 r_dihedral_angle_3_deg 13.806 r_dihedral_angle_2_deg 10.827 r_lrange_it 8.239 r_lrange_other 8.064 r_dihedral_angle_1_deg 6.912 r_scangle_it 4.859 r_scangle_other 4.858 r_mcangle_other 3.519 r_mcangle_it 3.518
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.233 r_dihedral_angle_3_deg 13.806 r_dihedral_angle_2_deg 10.827 r_lrange_it 8.239 r_lrange_other 8.064 r_dihedral_angle_1_deg 6.912 r_scangle_it 4.859 r_scangle_other 4.858 r_mcangle_other 3.519 r_mcangle_it 3.518 r_scbond_it 3.218 r_scbond_other 3.217 r_rigid_bond_restr 3.11 r_dihedral_angle_other_2_deg 2.22 r_mcbond_it 2.213 r_mcbond_other 2.209 r_angle_refined_deg 1.689 r_angle_other_deg 0.591 r_symmetry_nbd_refined 0.275 r_nbd_refined 0.228 r_symmetry_nbd_other 0.202 r_symmetry_xyhbond_nbd_refined 0.19 r_nbd_other 0.18 r_nbtor_refined 0.177 r_xyhbond_nbd_refined 0.152 r_ncsr_local_group_1 0.114 r_chiral_restr 0.081 r_symmetry_nbtor_other 0.08 r_bond_refined_d 0.009 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 3542 Nucleic Acid Atoms Solvent Atoms 264 Heterogen Atoms 70
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction Aimless data scaling MOLREP phasing