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Crystal structure of metal-citrate-binding mutant (D28A) protein (MctA) of ABC transporter endogenously bound to citrate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7F6E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 293 0.2 M ammonium phosphate dibasic, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.3 46.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.31 α = 90 b = 146.26 β = 99.89 c = 79.09 γ = 90
Symmetry Space Group P 1 21 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 IMAGE PLATE RIGAKU RAXIS IV VariMax HF 2019-12-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.15 73.24 95.5 0.091 0.1 0.041 0.997 12.7 5.5 52451
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 2.15 2.21 91.4 0.596 0.656 0.271 0.851 5.3
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 7F6E 2.15 73.24 49852 2565 95.32 0.1757 0.1737 0.1799 0.2144 0.2183 RANDOM 52.468
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] -0.51 0.14 1.72 -1.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.942 r_dihedral_angle_4_deg 17.338 r_dihedral_angle_3_deg 15.746 r_dihedral_angle_1_deg 6.76 r_angle_refined_deg 1.708 r_angle_other_deg 1.42 r_chiral_restr 0.085 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.942 r_dihedral_angle_4_deg 17.338 r_dihedral_angle_3_deg 15.746 r_dihedral_angle_1_deg 6.76 r_angle_refined_deg 1.708 r_angle_other_deg 1.42 r_chiral_restr 0.085 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7935 Nucleic Acid Atoms Solvent Atoms 452 Heterogen Atoms 68
Software Software Software Name Purpose HKL-3000 data collection MOSFLM data reduction Aimless data scaling PHASER phasing Coot model building REFMAC refinement PDB_EXTRACT data extraction