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Crystal structure of an orphan heme uptake protein (MhuP) of ABC transporter from Mycobacterium tuberculosis (Form I)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4PM4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 5 293 0.1 M citrate pH 5.0 and 20% PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.53 51.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.34 α = 90 b = 39.41 β = 108.34 c = 94.67 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++ Vari Max HF 2020-02-26 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 1.8 55.09 100 0.073 0.082 0.037 0.998 14.1 4.7 61369
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 1.8 1.84 99.8 0.465 0.527 0.245 0.819 4.5
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 4PM4 1.8 55.03 58301 3055 99.97 0.1569 0.1552 0.1675 0.1893 0.2012 RANDOM 24.433
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] -0.29 0.19 -0.42 0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.981 r_dihedral_angle_4_deg 18.876 r_dihedral_angle_3_deg 13.565 r_dihedral_angle_1_deg 6.656 r_angle_refined_deg 1.809 r_angle_other_deg 1.51 r_chiral_restr 0.095 r_bond_refined_d 0.014 r_gen_planes_refined 0.012 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.981 r_dihedral_angle_4_deg 18.876 r_dihedral_angle_3_deg 13.565 r_dihedral_angle_1_deg 6.656 r_angle_refined_deg 1.809 r_angle_other_deg 1.51 r_chiral_restr 0.095 r_bond_refined_d 0.014 r_gen_planes_refined 0.012 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4466 Nucleic Acid Atoms Solvent Atoms 696 Heterogen Atoms 50
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