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LeuD_1-168 small subunit of isopropylmalate isomerase (Rv2987c) from mycobacterium tuberculosis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3H5E PDB ENTRY 3H5E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8.5 293 0.2M lithium sulfate, 0.1M Tris-HCl pH 8.5, 20%(w/v) PEG 3350, VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.98 37.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.07 α = 90 b = 75.71 β = 103.22 c = 48.84 γ = 90
Symmetry Space Group P 1 21 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 225 mm CCD 2008-10-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X12 1.000 EMBL/DESY, HAMBURG X12
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 1.2 99 99.5 0.065 20.7 4 90248 90248 2 2
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) 1.2 1.22 91.9 0.296 3.8 3.4
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R PDB ENTRY 3H5E 1.2 13.42 88352 88352 1855 97.5 0.1298 0.1388 0.175 0.1779 random
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]
Coordinate Error Structure Solution Method Refinement High Resolution Refinement Low Resolution 24 2546.15 3024.55
RMS Deviations Key Refinement Restraint Deviation s_non_zero_chiral_vol 0.095 s_approx_iso_adps 0.094 s_zero_chiral_vol 0.082 s_similar_adp_cmpnt 0.052 s_anti_bump_dis_restr 0.035 s_angle_d 0.032 s_from_restr_planes 0.027 s_bond_d 0.013 s_similar_dist 0.008 s_rigid_bond_adp_cmpnt 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2595 Nucleic Acid Atoms Solvent Atoms 413 Heterogen Atoms 33
Software Software Software Name Purpose MAR345dtb data collection MOLREP phasing SHELXL-97 refinement HKL-2000 data reduction SCALEPACK data scaling