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2.1 Angstrom crystal structure of the L114P mutant of E. Coli KsgA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QYR PDB ENTRY 1QYR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 293 protein solution: 10 mg/mL ecKsgA, 50 mM Tris, pH 7.4, 50 mM ammonium chloride, 6 mM BME, reservoir solution: 80 mM MES/sodium, pH 6.5, 25% PEG5000 MME, 0.15 M ammonium sulfate , VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.43 49.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 239.007 α = 90 b = 38.534 β = 96.34 c = 64.752 γ = 90
Symmetry Space Group C 1 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 IMAGE PLATE RIGAKU RAXIS IV++ Rigaku Varimax Confocal Optics 2008-11-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.5418
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 2.1 34.65 95 0.064 12.7 3.98 34870 33415 37.8
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 2.18 93.9 0.335 4 3.95 3446
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 1QYR 2.1 28 34858 30071 3339 95.85 0.21787 0.21145 0.27566 0.2497 RANDOM 40.461
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] -2.2 0.28 0.85 1.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.136 r_dihedral_angle_4_deg 17.361 r_dihedral_angle_3_deg 16.529 r_scangle_it 8.202 r_scbond_it 6.053 r_dihedral_angle_1_deg 5.57 r_mcangle_it 3.092 r_mcbond_it 1.717 r_angle_refined_deg 1.106 r_chiral_restr 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.136 r_dihedral_angle_4_deg 17.361 r_dihedral_angle_3_deg 16.529 r_scangle_it 8.202 r_scbond_it 6.053 r_dihedral_angle_1_deg 5.57 r_mcangle_it 3.092 r_mcbond_it 1.717 r_angle_refined_deg 1.106 r_chiral_restr 0.07 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3964 Nucleic Acid Atoms Solvent Atoms 204 Heterogen Atoms 7
Software Software Software Name Purpose CrystalClear data collection PHASER phasing REFMAC refinement CrystalClear data reduction CrystalClear data scaling