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Crystal structure of an orphan heme uptake protein (MhuP) of ABC transporter from Mycobacterium tuberculosis (Form II)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7FHM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 277 0.2 M lithium sulfate monohydrate, 0.1 M sodium acetate trihydrate pH 4.6, 30% (w/v) PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.71 54.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 202.38 α = 90 b = 39.67 β = 113.38 c = 92.97 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 IMAGE PLATE RIGAKU RAXIS IV++ Vari Max HF 2020-01-01 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 2.01 53.25 99 0.117 0.135 0.067 0.985 9.8 3.9 45608
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 2.01 2.06 96.1 0.29 0.342 0.177 0.897 3.3
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 7FHM 2.01 53.25 43355 2243 98.96 0.1737 0.1714 0.1815 0.2152 0.2197 RANDOM 20.875
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] 0.74 0.84 -1.33 -0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.049 r_dihedral_angle_4_deg 19.383 r_dihedral_angle_3_deg 13.896 r_dihedral_angle_1_deg 6.674 r_angle_refined_deg 1.785 r_angle_other_deg 1.458 r_chiral_restr 0.089 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.049 r_dihedral_angle_4_deg 19.383 r_dihedral_angle_3_deg 13.896 r_dihedral_angle_1_deg 6.674 r_angle_refined_deg 1.785 r_angle_other_deg 1.458 r_chiral_restr 0.089 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4476 Nucleic Acid Atoms Solvent Atoms 621 Heterogen Atoms 41
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