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Crystal structure of KAI2-like protein from Striga (apo state 1)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3VXK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 278 sodium formate, Tris
Crystal Properties Matthews coefficient Solvent content 2.5 50.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.94 α = 90 b = 75.94 β = 90 c = 181.47 γ = 120
Symmetry Space Group P 61 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 IMAGE PLATE RIGAKU RAXIS VII 2013-09-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.542
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 2.02 19.74 99.6 36.2 18.7 21039
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 2.02 2.07 96.5 0.37 6.1 9.6
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 3VXK 2.02 19.74 19959 1080 99.57 0.1798 0.17743 0.1859 0.22462 0.2321 RANDOM 29.84
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] -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.653 r_dihedral_angle_4_deg 16.467 r_dihedral_angle_3_deg 12.676 r_dihedral_angle_1_deg 5.94 r_long_range_B_other 5.886 r_long_range_B_refined 5.877 r_scangle_other 3.179 r_mcangle_it 3.086 r_mcangle_other 3.085 r_scbond_it 1.914
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.653 r_dihedral_angle_4_deg 16.467 r_dihedral_angle_3_deg 12.676 r_dihedral_angle_1_deg 5.94 r_long_range_B_other 5.886 r_long_range_B_refined 5.877 r_scangle_other 3.179 r_mcangle_it 3.086 r_mcangle_other 3.085 r_scbond_it 1.914 r_scbond_other 1.913 r_mcbond_it 1.833 r_mcbond_other 1.832 r_angle_refined_deg 1.31 r_angle_other_deg 0.95 r_chiral_restr 0.077 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2121 Nucleic Acid Atoms Solvent Atoms 235 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing