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Crystal structure of metal-citrate-binding 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 6.5 293 0.2 M ammonium sulphate, 0.1 M MES mohohydrate pH 6.5, 30% (w/v) PEG monoethyl ether 5000
Crystal Properties Matthews coefficient Solvent content 2.29 46.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.55 α = 90 b = 145.11 β = 100.44 c = 79.24 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 2017-11-15 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 2.1 77.93 100 0.104 0.122 0.063 0.994 9.2 3.6 58898
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 2.1 2.16 99.7 0.439 0.522 0.278 0.833 3.4
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 2.1 72.66 55970 2893 99.97 0.1715 0.1693 0.1777 0.2129 0.2169 RANDOM 41.639
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] 0.18 0.96 0.15 -0.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.939 r_dihedral_angle_4_deg 18.122 r_dihedral_angle_3_deg 15.259 r_dihedral_angle_1_deg 6.713 r_angle_refined_deg 1.68 r_angle_other_deg 1.408 r_chiral_restr 0.078 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 32.939 r_dihedral_angle_4_deg 18.122 r_dihedral_angle_3_deg 15.259 r_dihedral_angle_1_deg 6.713 r_angle_refined_deg 1.68 r_angle_other_deg 1.408 r_chiral_restr 0.078 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 7902 Nucleic Acid Atoms Solvent Atoms 480 Heterogen Atoms 102
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