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Shikimate kinase from Mycobacterium tuberculosis in complex with MgATP, open LID (conf. B)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2IYV PDB ENTRY 2IYV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 25%(W/V) PEG 3000, 100MM MES PH 6.5
Crystal Properties Matthews coefficient Solvent content 2 39.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.97 α = 90 b = 44.581 β = 109.7 c = 51.762 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 MARRESEARCH MIRRORS 2006-08-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MPG/DESY, HAMBURG BEAMLINE BW6 MPG/DESY, HAMBURG BW6
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 1.85 19.47 98.3 0.098 10.86 3.55 14156
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 1.85 1.99 98.5 0.42 3.35 3.5
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 (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 2IYV 1.85 19.47 13422 734 98.3 0.163 0.161 0.1713 0.2 0.216 RANDOM 17.05
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] 0.62 0.64 -0.39 0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.55 r_dihedral_angle_4_deg 15.487 r_dihedral_angle_3_deg 12.395 r_scangle_it 5.389 r_dihedral_angle_1_deg 4.708 r_angle_other_deg 3.542 r_scbond_it 3.19 r_mcangle_it 2.002 r_angle_refined_deg 1.322 r_mcbond_it 1.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.55 r_dihedral_angle_4_deg 15.487 r_dihedral_angle_3_deg 12.395 r_scangle_it 5.389 r_dihedral_angle_1_deg 4.708 r_angle_other_deg 3.542 r_scbond_it 3.19 r_mcangle_it 2.002 r_angle_refined_deg 1.322 r_mcbond_it 1.12 r_symmetry_vdw_other 0.257 r_nbd_other 0.238 r_nbd_refined 0.218 r_nbtor_refined 0.163 r_xyhbond_nbd_refined 0.151 r_symmetry_vdw_refined 0.14 r_symmetry_hbond_refined 0.131 r_nbtor_other 0.1 r_chiral_restr 0.066 r_bond_refined_d 0.01 r_gen_planes_other 0.005 r_gen_planes_refined 0.004 r_bond_other_d r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1318 Nucleic Acid Atoms Solvent Atoms 206 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling