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Crystal Structure of Rv1284 from Mycobacterium tuberculosis in Complex with Thiocyanate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1G5C PDB entry 1G5C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 sodium thiocyanate, polyethylene glycol 2000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal Properties Matthews coefficient Solvent content 2 37.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.164 α = 90 b = 154.074 β = 90 c = 156.943 γ = 90
Symmetry Space Group F 2 2 2
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 4 Sagitally focusing Ge(220) and a multilayer 2003-09-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.934 ESRF ID14-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2 44.3 94.6 0.085 0.079 20.3 7.4 38625 26.923
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.02 93.7 0.434 0.399 6.3 6.5 1363
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 (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 PDB entry 1G5C 2 42.26 36658 1946 94.18 0.18314 0.18314 0.18082 0.1944 0.22645 0.2321 RANDOM 23.167
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] 0.36 -0.28 -0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.244 r_dihedral_angle_4_deg 14.634 r_dihedral_angle_3_deg 13.279 r_dihedral_angle_1_deg 5.982 r_scangle_it 2.828 r_scbond_it 1.788 r_angle_refined_deg 1.305 r_mcangle_it 0.965 r_mcbond_it 0.523 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.244 r_dihedral_angle_4_deg 14.634 r_dihedral_angle_3_deg 13.279 r_dihedral_angle_1_deg 5.982 r_scangle_it 2.828 r_scbond_it 1.788 r_angle_refined_deg 1.305 r_mcangle_it 0.965 r_mcbond_it 0.523 r_nbtor_refined 0.302 r_nbd_refined 0.223 r_symmetry_vdw_refined 0.217 r_xyhbond_nbd_refined 0.13 r_symmetry_hbond_refined 0.097 r_chiral_restr 0.084 r_metal_ion_refined 0.03 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5084 Nucleic Acid Atoms Solvent Atoms 268 Heterogen Atoms 19
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling AMoRE phasing