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Chlororaphen Synthase from Pseudomonas chlororaphis (Pc-ChloS) in complex with pyrophosphate
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 5.5 293 0.1 M (NH4)2CO3, 0.1 M MES, 17% PEG 10000
Crystal Properties Matthews coefficient Solvent content 2.24 45.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.49 α = 105.08 b = 52.6 β = 93.26 c = 68.96 γ = 92.02
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 16M 2025-03-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 1.0597 PETRA III, EMBL c/o DESY P13 (MX1)
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 30 94.1 0.096 8.3 3.2 42646
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 2.1 93.8 0.763 2 3.3
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 30 40505 2132 94.19 0.18417 0.18198 0.1905 0.22549 0.2349 RANDOM 31.705
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] -1.44 1.15 -0.08 0.01 -1.34 1.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.463 r_dihedral_angle_4_deg 15.482 r_dihedral_angle_3_deg 12.788 r_dihedral_angle_1_deg 5.268 r_long_range_B_refined 2.945 r_long_range_B_other 2.543 r_mcangle_it 1.241 r_mcangle_other 1.241 r_angle_refined_deg 1.11 r_scangle_other 1.108
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.463 r_dihedral_angle_4_deg 15.482 r_dihedral_angle_3_deg 12.788 r_dihedral_angle_1_deg 5.268 r_long_range_B_refined 2.945 r_long_range_B_other 2.543 r_mcangle_it 1.241 r_mcangle_other 1.241 r_angle_refined_deg 1.11 r_scangle_other 1.108 r_angle_other_deg 1.098 r_mcbond_it 0.857 r_mcbond_other 0.856 r_scbond_it 0.803 r_scbond_other 0.803 r_rigid_bond_restr 0.286 r_chiral_restr 0.046 r_bond_refined_d 0.002 r_gen_planes_refined 0.002 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5142 Nucleic Acid Atoms Solvent Atoms 384 Heterogen Atoms 97
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling PHASER phasing