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VanYB in complex with D-Alanine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5ZHF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 295 PEG 1500, sodium acetate
Crystal Properties Matthews coefficient Solvent content 2.28 45.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.368 α = 90 b = 40.83 β = 109.08 c = 114.672 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 ADSC QUANTUM 270 2018-05-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 0.97934 PAL/PLS 7A (6B, 6C1)
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 2.29 50 99.1 0.091 11.1 3.6 17526
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 2.29 2.33 0.477
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 5ZHF 2.26 36.46 16380 880 96.37 0.20523 0.20159 0.2117 0.2763 0.2802 RANDOM 34.716
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] 0.73 0.39 -0.78 -0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.519 r_dihedral_angle_4_deg 27.68 r_dihedral_angle_3_deg 16.546 r_dihedral_angle_1_deg 6.921 r_long_range_B_refined 5.669 r_long_range_B_other 5.668 r_scangle_other 3.959 r_mcangle_it 3.454 r_mcangle_other 3.453 r_scbond_it 2.508
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.519 r_dihedral_angle_4_deg 27.68 r_dihedral_angle_3_deg 16.546 r_dihedral_angle_1_deg 6.921 r_long_range_B_refined 5.669 r_long_range_B_other 5.668 r_scangle_other 3.959 r_mcangle_it 3.454 r_mcangle_other 3.453 r_scbond_it 2.508 r_scbond_other 2.508 r_mcbond_other 2.267 r_mcbond_it 2.266 r_angle_refined_deg 1.36 r_angle_other_deg 0.907 r_chiral_restr 0.064 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2941 Nucleic Acid Atoms Solvent Atoms 22 Heterogen Atoms 86
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing