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C-terminal domain of KipI from Bacillus subtilis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PHC PDB entry 2PHC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.9 293 15% PEG 8000, 20% glycerol, 40mM potassium phosphate, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.61 52.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.909 α = 90 b = 84.417 β = 90 c = 84.409 γ = 90
Symmetry Space Group P 21 21 21
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 MAR scanner 345 mm plate Osmic mirror optics 2008-05-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 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 3 17 99.8 0.14 6.7 6 6751 6738 -3 -3 78
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) 3 3.11 98.4 0.66 1.5 4.6 629
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 2PHC 3.01 16.88 6399 6375 321 99.63 0.26747 0.26747 0.26354 0.2654 0.34378 0.3481 RANDOM 37.673
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] 3.09 -1.64 -1.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.906 r_dihedral_angle_3_deg 20.449 r_dihedral_angle_4_deg 11.555 r_dihedral_angle_1_deg 7.222 r_scangle_it 4.474 r_scbond_it 3.013 r_mcangle_it 2.188 r_mcbond_it 1.271 r_angle_refined_deg 1.219 r_angle_other_deg 0.882
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.906 r_dihedral_angle_3_deg 20.449 r_dihedral_angle_4_deg 11.555 r_dihedral_angle_1_deg 7.222 r_scangle_it 4.474 r_scbond_it 3.013 r_mcangle_it 2.188 r_mcbond_it 1.271 r_angle_refined_deg 1.219 r_angle_other_deg 0.882 r_symmetry_hbond_refined 0.293 r_mcbond_other 0.251 r_nbd_refined 0.214 r_nbd_other 0.185 r_nbtor_refined 0.185 r_symmetry_vdw_other 0.182 r_xyhbond_nbd_refined 0.161 r_symmetry_vdw_refined 0.118 r_symmetry_hbond_other 0.1 r_nbtor_other 0.089 r_chiral_restr 0.069 r_bond_refined_d 0.009 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1635 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MAR345dtb data collection DENZO data reduction SCALEPACK data scaling PHASER phasing