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PBP AccA from A. vitis S4 in complex with L-arabinose-2-phosphate (A2P)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4ZEI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 292 PEG 8000, HEPES
Crystal Properties Matthews coefficient Solvent content 2.02 39.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.08 α = 90 b = 61.03 β = 90 c = 152.81 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 9M 2022-06-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.983997 SOLEIL PROXIMA 2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.4 50 99.8 0.045 1 30.57 6.24 86791 18.83
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.4 1.49 0.881 0.964
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.404 14.14 86686 4334 99.9 0.1741 0.1731 0.1696 0.1924 0.1897 RANDOM 26.35
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] -1.1726 1.8262 -0.6536
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 14.44 t_omega_torsion 5.29 t_angle_deg 1.16 t_bond_d 0.011 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 14.44 t_omega_torsion 5.29 t_angle_deg 1.16 t_bond_d 0.011 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3820 Nucleic Acid Atoms Solvent Atoms 560 Heterogen Atoms 19
Software Software Software Name Purpose BUSTER refinement XDS data reduction XSCALE data scaling PHASER phasing