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The structure of the apo-AglA from Streptomyces monomycini
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 289.15 0.05 M Magnesium Chloride Hexahydrate, 0.1 M HEPES (pH 7.5) and 30% PEG 550 MME
Crystal Properties Matthews coefficient Solvent content 2.81 56.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.251 α = 90 b = 77.251 β = 90 c = 116.086 γ = 90
Symmetry Space Group P 43 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 PIXEL DECTRIS PILATUS 6M 2022-08-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.97853 SSRF BL18U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.056 46.45 99.92 0.997 4.35 3.3 90468
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.06 2.15 0.0175
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 2.06 46.45 72421 1068 99.91 0.16191 0.1593 0.1712 0.21391 0.2218 RANDOM 48.233
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] 0.04 0.04 -0.09
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 19.007 r_long_range_B_other 18.971 r_scangle_other 15.821 r_dihedral_angle_3_deg 14.888 r_mcangle_other 12.288 r_mcangle_it 12.285 r_scbond_it 11.239 r_scbond_other 11.231 r_mcbond_it 8.74 r_mcbond_other 8.736
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 19.007 r_long_range_B_other 18.971 r_scangle_other 15.821 r_dihedral_angle_3_deg 14.888 r_mcangle_other 12.288 r_mcangle_it 12.285 r_scbond_it 11.239 r_scbond_other 11.231 r_mcbond_it 8.74 r_mcbond_other 8.736 r_dihedral_angle_2_deg 8.363 r_dihedral_angle_1_deg 6.632 r_rigid_bond_restr 4.582 r_angle_refined_deg 1.948 r_angle_other_deg 0.684 r_chiral_restr 0.093 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_gen_planes_other 0.006 r_bond_other_d 0.001 r_dihedral_angle_4_deg 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1938 Nucleic Acid Atoms Solvent Atoms 63 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement XDS data scaling XDS data reduction PHASER phasing