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Crystal structure of BcABA3 from Botrytis cinerea
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8ZAD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 2% Tacsimate pH 7.0, 0.1 M HEPES pH 7.5, 25% PEG 3350
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.203 α = 90 b = 166.89 β = 90 c = 57.151 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 MX300-HS 2019-02-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE TPS 05A 0.9998 NSRRC TPS 05A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.45 25 99.1 0.049 0.053 0.018 0.998 12.3 8.5 29294
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.45 2.54 91.9 0.217 0.236 0.089 0.981 6.3
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 8ZAD 2.45 24.47 27799 1449 98.7 0.18727 0.18363 0.25401 0.2594 RANDOM 56.798
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] -2.96 -2.11 5.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.969 r_dihedral_angle_3_deg 17.657 r_dihedral_angle_4_deg 15.818 r_long_range_B_refined 9.734 r_long_range_B_other 9.733 r_scangle_other 7.62 r_mcangle_it 7.343 r_mcangle_other 7.342 r_dihedral_angle_1_deg 6.788 r_mcbond_it 5.165
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.969 r_dihedral_angle_3_deg 17.657 r_dihedral_angle_4_deg 15.818 r_long_range_B_refined 9.734 r_long_range_B_other 9.733 r_scangle_other 7.62 r_mcangle_it 7.343 r_mcangle_other 7.342 r_dihedral_angle_1_deg 6.788 r_mcbond_it 5.165 r_mcbond_other 5.152 r_scbond_it 5.08 r_scbond_other 5.08 r_angle_refined_deg 1.521 r_angle_other_deg 1.247 r_chiral_restr 0.07 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5793 Nucleic Acid Atoms Solvent Atoms 209 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling HKL-2000 data reduction PHASER phasing