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FGD1 (Rv0407) from Mycobacterium tuberculosis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other an in-house apo structure (itself solved by Se-MAD)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 291 1.4M tri-sodium citrate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.07 40.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.078 α = 90 b = 89.907 β = 90 c = 80.146 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 IMAGE PLATE MAR scanner 345 mm plate osmic 2007-08-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.5418
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 1.95 25.18 96.7 0.114 17.6 9.8 47109 47019
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2.06 92.6 0.484 1.2 2 13127
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 an in-house apo structure (itself solved by Se-MAD) 1.95 24.65 44565 44565 2330 96.43 0.19385 0.19385 0.19174 0.1991 0.23434 0.2114 RANDOM 20.083
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] -0.63 0.46 0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.443 r_dihedral_angle_4_deg 16.448 r_dihedral_angle_3_deg 15.301 r_dihedral_angle_1_deg 6.494 r_scangle_it 2.587 r_scbond_it 2.072 r_angle_refined_deg 1.646 r_mcangle_it 1.21 r_mcbond_it 0.752 r_symmetry_hbond_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.443 r_dihedral_angle_4_deg 16.448 r_dihedral_angle_3_deg 15.301 r_dihedral_angle_1_deg 6.494 r_scangle_it 2.587 r_scbond_it 2.072 r_angle_refined_deg 1.646 r_mcangle_it 1.21 r_mcbond_it 0.752 r_symmetry_hbond_refined 0.307 r_nbtor_refined 0.301 r_symmetry_vdw_refined 0.248 r_nbd_refined 0.199 r_xyhbond_nbd_refined 0.135 r_chiral_restr 0.116 r_bond_refined_d 0.014 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5140 Nucleic Acid Atoms Solvent Atoms 195 Heterogen Atoms 114
Software Software Software Name Purpose REFMAC refinement MAR345dtb data collection MOSFLM data reduction SCALA data scaling REFMAC phasing