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Crystal structure of Rv3671c protease from M. tuberculosis, active form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1L1J PDB entry 1L1J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.25 293 Reservoir: 0.05 M sodium acetate pH 5.25, 1.96 M sodium formate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.47 50.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.678 α = 90 b = 64.678 β = 90 c = 98.655 γ = 120
Symmetry Space Group P 31 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 MARMOSAIC 300 mm CCD 2008-11-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 0.99986 APS 21-ID-D
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 1.3 50 99.5 0.067 10.1 59589 59291 3 3
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) 1.3 1.35 100 0.62 3.2 6.7 5868
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1L1J 1.3 30 59589 56042 2988 99.44 0.16628 0.16628 0.16455 0.19928 0.2036 RANDOM 20.07
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] 0.35 0.17 0.35 -0.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.152 r_dihedral_angle_4_deg 17.318 r_dihedral_angle_3_deg 10.386 r_dihedral_angle_1_deg 6.193 r_sphericity_bonded 5.149 r_scangle_it 4.534 r_sphericity_free 4.435 r_scbond_it 4.175 r_rigid_bond_restr 3.823 r_mcangle_it 2.096
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.152 r_dihedral_angle_4_deg 17.318 r_dihedral_angle_3_deg 10.386 r_dihedral_angle_1_deg 6.193 r_sphericity_bonded 5.149 r_scangle_it 4.534 r_sphericity_free 4.435 r_scbond_it 4.175 r_rigid_bond_restr 3.823 r_mcangle_it 2.096 r_angle_refined_deg 1.454 r_mcbond_it 1.407 r_nbtor_refined 0.311 r_symmetry_vdw_refined 0.236 r_nbd_refined 0.215 r_symmetry_hbond_refined 0.173 r_xyhbond_nbd_refined 0.172 r_chiral_restr 0.092 r_bond_refined_d 0.01 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1617 Nucleic Acid Atoms Solvent Atoms 382 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling