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Crystal structure of the YgjG-protein A-Zpa963-calmodulin complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4UOY 4UOY, 2M5A, 3DVE experimental model PDB 2M5A 4UOY, 2M5A, 3DVE experimental model PDB 3DVE 4UOY, 2M5A, 3DVE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 296 0.1M HEPES pH 7.5, 20.7% PEG 300, 99mM calcium chloride
Crystal Properties Matthews coefficient Solvent content 3.61 65.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.489 α = 84.84 b = 155.376 β = 89.68 c = 155.491 γ = 89.56
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 80 CCD ADSC QUANTUM 315 2016-10-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 5C (4A) 0.97934 PAL/PLS 5C (4A)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.6 50 90.5 14.6 2.3 210653
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.69 83.4 1.2 2
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 4UOY, 2M5A, 3DVE 2.57 50 189578 21075 89.49 0.20754 0.20377 0.2045 0.24092 0.2416 RANDOM 87.987
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] 4.04 0.33 -0.72 -1.82 2.49 -1.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.544 r_dihedral_angle_4_deg 20.137 r_dihedral_angle_3_deg 16.835 r_sphericity_bonded 14.407 r_long_range_B_refined 6.219 r_rigid_bond_restr 5.384 r_dihedral_angle_1_deg 5.146 r_mcangle_it 4.896 r_scbond_it 4.405 r_mcbond_it 3.686
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.544 r_dihedral_angle_4_deg 20.137 r_dihedral_angle_3_deg 16.835 r_sphericity_bonded 14.407 r_long_range_B_refined 6.219 r_rigid_bond_restr 5.384 r_dihedral_angle_1_deg 5.146 r_mcangle_it 4.896 r_scbond_it 4.405 r_mcbond_it 3.686 r_angle_refined_deg 1.232 r_chiral_restr 0.07 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_sphericity_free
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 37116 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing