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Shikimate kinase from Mycobacterium tuberculosis in complex with ADP, open LID (conf. B)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2IYQ PDB ENTRY 2IYQ
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 37.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.618 α = 90 b = 44.193 β = 109.13 c = 51.289 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 2001-07-12 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 1.35 19.28 97.2 0.07 7.35 2.51 34977
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 1.35 1.38 92.8 0.57 1.64 2.4
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 2IYQ 1.35 19.28 33221 1756 97.2 0.14 0.138 0.1529 0.178 0.199 RANDOM 14.5
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] 1.98 0.84 -0.97 -0.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.377 r_dihedral_angle_4_deg 15.859 r_dihedral_angle_3_deg 13.489 r_scangle_it 6.689 r_scbond_it 5.07 r_dihedral_angle_1_deg 5.055 r_mcangle_it 4.525 r_mcbond_it 4.098 r_angle_refined_deg 1.517 r_angle_other_deg 0.845
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.377 r_dihedral_angle_4_deg 15.859 r_dihedral_angle_3_deg 13.489 r_scangle_it 6.689 r_scbond_it 5.07 r_dihedral_angle_1_deg 5.055 r_mcangle_it 4.525 r_mcbond_it 4.098 r_angle_refined_deg 1.517 r_angle_other_deg 0.845 r_symmetry_vdw_other 0.244 r_nbd_refined 0.232 r_nbd_other 0.203 r_nbtor_refined 0.171 r_xyhbond_nbd_refined 0.155 r_symmetry_vdw_refined 0.138 r_chiral_restr 0.09 r_nbtor_other 0.082 r_symmetry_hbond_refined 0.077 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 1334 Nucleic Acid Atoms Solvent Atoms 185 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing