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Crystal structure of Spire KIND domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3R7G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION VAPOR DIFFUSION
Crystal Properties Matthews coefficient Solvent content 2.48 50.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.328 α = 90 b = 66.265 β = 103 c = 100.852 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 90 CCD ADSC QUANTUM 315 2009-02-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.97918 APS 24-ID-E
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 3.2 41 94.3 0.061 14 5.3 14983
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 3r7g 3.2 25 14116 743 94.19 0.26325 0.2606 0.2593 0.31501 0.3185 RANDOM 99.679
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] -6.58 1.69 -6.72 14.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.424 r_dihedral_angle_3_deg 20.6 r_dihedral_angle_4_deg 17.987 r_scangle_it 7.794 r_dihedral_angle_1_deg 5.931 r_mcangle_it 4.777 r_scbond_it 4.429 r_mcbond_it 2.455 r_angle_refined_deg 1.332 r_chiral_restr 0.086
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.424 r_dihedral_angle_3_deg 20.6 r_dihedral_angle_4_deg 17.987 r_scangle_it 7.794 r_dihedral_angle_1_deg 5.931 r_mcangle_it 4.777 r_scbond_it 4.429 r_mcbond_it 2.455 r_angle_refined_deg 1.332 r_chiral_restr 0.086 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 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 4845 Nucleic Acid Atoms Solvent Atoms 5 Heterogen Atoms
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling