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Crystal structure of mutant nitrobindin M75A/H76L/Q96C/M148L/H158A (NB11) from Arabidopsis thaliana
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2A13
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.3 293 Tris-HCl buffer, polyethylene glycol 2000
Crystal Properties Matthews coefficient Solvent content 2.22 44.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.654 α = 90 b = 79.285 β = 90 c = 36.409 γ = 90
Symmetry Space Group P 21 21 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 RAYONIX MX300HE 2014-05-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.90000 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 50 98.3 0.051 42.7 10.3 92122
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 1 1.04 95.7 4.2
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 2A13 1 47.67 87472 4620 98.17 0.12375 0.12312 0.1246 0.13593 0.1367 RANDOM 18.747
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] -0.15 0.09 0.05
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 35.242 r_dihedral_angle_2_deg 33.096 r_dihedral_angle_4_deg 18.272 r_sphericity_bonded 11.124 r_dihedral_angle_3_deg 10.747 r_dihedral_angle_1_deg 6.884 r_rigid_bond_restr 5.833 r_long_range_B_refined 4.762 r_long_range_B_other 4.206 r_scangle_other 4.121
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 35.242 r_dihedral_angle_2_deg 33.096 r_dihedral_angle_4_deg 18.272 r_sphericity_bonded 11.124 r_dihedral_angle_3_deg 10.747 r_dihedral_angle_1_deg 6.884 r_rigid_bond_restr 5.833 r_long_range_B_refined 4.762 r_long_range_B_other 4.206 r_scangle_other 4.121 r_scbond_it 3.28 r_scbond_other 3.276 r_angle_refined_deg 2.02 r_angle_other_deg 1.773 r_mcangle_it 1.701 r_mcangle_other 1.7 r_mcbond_other 1.314 r_mcbond_it 1.313 r_chiral_restr 0.139 r_bond_refined_d 0.023 r_gen_planes_refined 0.012 r_gen_planes_other 0.012 r_bond_other_d 0.001 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1190 Nucleic Acid Atoms Solvent Atoms 195 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement HKL-2000 data processing PHASER phasing Coot model building HKL-2000 data reduction