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Crystal structure of NpuDnaB intein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MI8 PDB ENTRY 1MI8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 293 0.1 M Bis-Tris, pH 5.5, 3.0 M NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K
Crystal Properties Matthews coefficient Solvent content 3.67 66.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.054 α = 90 b = 61.054 β = 90 c = 122.179 γ = 90
Symmetry Space Group P 43 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 100 CCD ADSC QUANTUM 210 2011-06-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 1.0 ESRF ID14-1
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 1.4 61.05 100 0.081 46443 46443 2 2
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 1.4 1.45 100 0.932
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1MI8 1.4 61.05 46443 45373 948 99.83 0.16179 0.16123 0.1561 0.18906 0.1849 RANDOM 22.405
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] 0.55 0.55 -1.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.34 r_dihedral_angle_4_deg 24.053 r_dihedral_angle_3_deg 12.113 r_dihedral_angle_1_deg 6.077 r_scangle_it 4.142 r_scbond_it 2.647 r_mcangle_it 2.163 r_angle_refined_deg 1.288 r_mcbond_it 1.276 r_rigid_bond_restr 1.265
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.34 r_dihedral_angle_4_deg 24.053 r_dihedral_angle_3_deg 12.113 r_dihedral_angle_1_deg 6.077 r_scangle_it 4.142 r_scbond_it 2.647 r_mcangle_it 2.163 r_angle_refined_deg 1.288 r_mcbond_it 1.276 r_rigid_bond_restr 1.265 r_chiral_restr 0.092 r_bond_refined_d 0.009 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1094 Nucleic Acid Atoms Solvent Atoms 278 Heterogen Atoms 19
Software Software Software Name Purpose REFMAC refinement PHASES phasing PHENIX refinement HKL-2000 data reduction SCALEPACK data scaling ADSC data collection