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Structure of the WT-Phycoerythrobilin Synthase PebS from the Cyanophage P-SSM2 in Complex with the bound Substrate Biliverdin IXa
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VCK PDB ENTRY 2VCK
Crystallization Crystal Properties Matthews coefficient Solvent content 2.5 52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.99 α = 75.53 b = 70.04 β = 70.74 c = 81.67 γ = 71.13
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 MARRESEARCH MIRRORS 2007-10-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA SLS X06SA
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 2.1 48 97.5 0.08 12.8 4.3 60138
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 2.1 2.3 96.9 0.3 5.3 4.4
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 PDB ENTRY 2VCK 2.1 47.62 56953 3185 100 0.23 0.226 0.2263 0.285 0.2836 RANDOM 28.99
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] -0.51 -0.59 0.4 3.76 -1.08 -2.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_4_deg 21.139 r_dihedral_angle_3_deg 17.324 r_dihedral_angle_1_deg 7.657 r_scangle_it 2.288 r_scbond_it 1.607 r_angle_refined_deg 1.516 r_mcangle_it 1.369 r_mcbond_it 0.809 r_nbtor_refined 0.32 r_symmetry_vdw_refined 0.274
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_4_deg 21.139 r_dihedral_angle_3_deg 17.324 r_dihedral_angle_1_deg 7.657 r_scangle_it 2.288 r_scbond_it 1.607 r_angle_refined_deg 1.516 r_mcangle_it 1.369 r_mcbond_it 0.809 r_nbtor_refined 0.32 r_symmetry_vdw_refined 0.274 r_nbd_refined 0.224 r_xyhbond_nbd_refined 0.21 r_symmetry_hbond_refined 0.208 r_chiral_restr 0.118 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7010 Nucleic Acid Atoms Solvent Atoms 339 Heterogen Atoms 172
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing