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Crystal structure of Necrosis and Ethylene inducing Protein 2 from the causal agent of cocoa's Witches Broom disease
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GNU PDB ENTRY 3GNU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 291 100 mM Sodium Acetate pH 5.0
20% PEG 6000
20 mM ZnCl2, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.46 49.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.48 α = 90 b = 44.21 β = 110.04 c = 60.17 γ = 90
Symmetry Space Group C 1 2 1
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 MAR CCD 165 mm 2011-06-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE D03B-MX1 1.608 LNLS D03B-MX1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.8 14.52 93.9 0.049 0.049 7.9 5.1 20582 19327 2 2 14.02
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.9 84.2 0.17 0.17 7.9 3.7
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 3GNU 1.8 14.52 19625 18298 1006 93.24 0.14226 0.13929 0.1394 0.19578 0.1961 RANDOM 15.413
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] -0.08 -0.2 0.42 -0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.747 r_dihedral_angle_4_deg 15.437 r_dihedral_angle_3_deg 12.04 r_dihedral_angle_1_deg 6.557 r_scangle_it 3.645 r_scbond_it 2.624 r_angle_refined_deg 1.869 r_mcangle_it 1.861 r_mcbond_it 1.178 r_chiral_restr 0.146
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.747 r_dihedral_angle_4_deg 15.437 r_dihedral_angle_3_deg 12.04 r_dihedral_angle_1_deg 6.557 r_scangle_it 3.645 r_scbond_it 2.624 r_angle_refined_deg 1.869 r_mcangle_it 1.861 r_mcbond_it 1.178 r_chiral_restr 0.146 r_bond_refined_d 0.023 r_gen_planes_refined 0.011 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 1590 Nucleic Acid Atoms Solvent Atoms 358 Heterogen Atoms 2
Software Software Software Name Purpose MAR345 data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling