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Structure of F420 binding protein, MSMEG_6526, from Mycobacterium smegmatis with F420 bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4ZKY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 100 mM Sodium Acetate pH 4.6
20 mM Calcium Chloride
28% MPD
Crystal Properties Matthews coefficient Solvent content 2.42 49.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 139.951 α = 90 b = 84.241 β = 90.85 c = 75.98 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 CCD ADSC QUANTUM 210r 2015-10-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 0.9501 Australian Synchrotron MX1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.7 75.97 100 0.122 6.6 3.7 96899
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 9.31
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 4ZKY 1.7 75.97 91915 4905 99.92 0.1914 0.1894 0.1981 0.23081 0.2409 RANDOM 20.502
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] -0.01 0.03 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.986 r_dihedral_angle_4_deg 21.515 r_dihedral_angle_3_deg 12.654 r_dihedral_angle_1_deg 6.825 r_long_range_B_refined 6.508 r_long_range_B_other 6.374 r_scangle_other 4.553 r_angle_other_deg 3.648 r_mcangle_it 3.01 r_mcangle_other 3.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.986 r_dihedral_angle_4_deg 21.515 r_dihedral_angle_3_deg 12.654 r_dihedral_angle_1_deg 6.825 r_long_range_B_refined 6.508 r_long_range_B_other 6.374 r_scangle_other 4.553 r_angle_other_deg 3.648 r_mcangle_it 3.01 r_mcangle_other 3.01 r_scbond_it 2.947 r_scbond_other 2.947 r_mcbond_it 2.039 r_mcbond_other 2.039 r_angle_refined_deg 1.831 r_chiral_restr 0.175 r_gen_planes_other 0.022 r_bond_refined_d 0.018 r_gen_planes_refined 0.012 r_bond_other_d r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6544 Nucleic Acid Atoms Solvent Atoms 542 Heterogen Atoms 276
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling MOLREP phasing