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2.05 a Crystal Structure of CysM from Mycobacterium Tuberculosis - Open and Closed Conformations
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DKI PDB ENTRY 3DKI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.4 293 0.1M Tris-HCl pH 7.5, 0.1M K2HPO4, 4.3M NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.37 48.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.933 α = 90 b = 89.142 β = 90 c = 99.382 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 CCD ADSC QUANTUM 315 torodial focusing mirror 2008-02-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.93400 ESRF ID14-4
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 2.05 89.15 98.1 0.086 0.086 12.2 3.8 41528 41528 2 2 23.8
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) 2.05 2.16 97 0.637 0.554 2 3.8 5922
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3DKI 2.05 50 41528 39379 2092 97.66 0.20041 0.19787 0.24671 0.2581 RANDOM 23.818
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] 0.34 -0.55 0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.815 r_dihedral_angle_3_deg 18.276 r_dihedral_angle_4_deg 16.958 r_dihedral_angle_1_deg 6.82 r_scangle_it 2.348 r_scbond_it 1.676 r_angle_refined_deg 1.484 r_mcangle_it 1.068 r_angle_other_deg 1.05 r_mcbond_it 0.914
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.815 r_dihedral_angle_3_deg 18.276 r_dihedral_angle_4_deg 16.958 r_dihedral_angle_1_deg 6.82 r_scangle_it 2.348 r_scbond_it 1.676 r_angle_refined_deg 1.484 r_mcangle_it 1.068 r_angle_other_deg 1.05 r_mcbond_it 0.914 r_symmetry_vdw_other 0.258 r_symmetry_hbond_refined 0.251 r_nbd_other 0.204 r_nbd_refined 0.202 r_symmetry_vdw_refined 0.19 r_xyhbond_nbd_refined 0.185 r_nbtor_refined 0.173 r_mcbond_other 0.143 r_chiral_restr 0.099 r_xyhbond_nbd_other 0.093 r_nbtor_other 0.089 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4801 Nucleic Acid Atoms Solvent Atoms 324 Heterogen Atoms
Software Software Software Name Purpose DNA data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling