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Crystal Structure of IphB from Comamonas testosteroni KF1 in complex with NADP and 3,4-dihydroxybenzoic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7XH1
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 44.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.703 α = 90 b = 152.275 β = 90 c = 74.113 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 2022-12-19 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 1.54 26.571 99.73 0.995 7.61 6.1 65908
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 1.54 1.56 0.28
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.54 26.57 65908 3355 99.71 0.1674 0.1807 0.1915 0.2015 RANDOM 13.51
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] 0.12 0.04 -0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.507 r_dihedral_angle_1_deg 6.614 r_scangle_it 5.757 r_scangle_other 5.756 r_dihedral_angle_2_deg 5.731 r_scbond_it 3.965 r_scbond_other 3.964 r_mcangle_other 2.836 r_mcangle_it 2.834 r_mcbond_it 1.993
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.507 r_dihedral_angle_1_deg 6.614 r_scangle_it 5.757 r_scangle_other 5.756 r_dihedral_angle_2_deg 5.731 r_scbond_it 3.965 r_scbond_other 3.964 r_mcangle_other 2.836 r_mcangle_it 2.834 r_mcbond_it 1.993 r_mcbond_other 1.992 r_angle_refined_deg 1.647 r_angle_other_deg 0.553 r_nbd_refined 0.222 r_nbtor_refined 0.18 r_nbd_other 0.166 r_xyhbond_nbd_refined 0.152 r_chiral_restr 0.081 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbtor_other 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_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3503 Nucleic Acid Atoms Solvent Atoms 168 Heterogen Atoms 67
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction Aimless data scaling MOLREP phasing