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Structure of 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 2VCL PDB ENTRY 2VCL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 HANGING DROP VAPOUR DIFFUSION PROTEIN:RESERVOIR 2:1, pH 5.5
Crystal Properties Matthews coefficient Solvent content 2.5 51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.56 α = 92.26 b = 67.57 β = 109.07 c = 81.28 γ = 106.58
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 2007-06-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA SLS X10SA
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 1.8 49 97.1 0.11 13.2 8.1 91993 5 21
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 1.8 1.9 95.9 0.42 5 8.2
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2VCL 1.8 49.21 87171 4819 100 0.187 0.184 0.225 0.2253 RANDOM 15.29
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] 0.08 0.08 0.17 0.57 0.45 -0.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_4_deg 18.258 r_dihedral_angle_3_deg 15.349 r_dihedral_angle_1_deg 6.81 r_scangle_it 3.248 r_scbond_it 2.233 r_mcangle_it 1.522 r_angle_refined_deg 1.468 r_mcbond_it 1.061 r_nbtor_refined 0.316 r_nbd_refined 0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_4_deg 18.258 r_dihedral_angle_3_deg 15.349 r_dihedral_angle_1_deg 6.81 r_scangle_it 3.248 r_scbond_it 2.233 r_mcangle_it 1.522 r_angle_refined_deg 1.468 r_mcbond_it 1.061 r_nbtor_refined 0.316 r_nbd_refined 0.2 r_symmetry_hbond_refined 0.178 r_xyhbond_nbd_refined 0.171 r_symmetry_vdw_refined 0.165 r_chiral_restr 0.107 r_dihedral_angle_2_deg 0.021 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_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 6928 Nucleic Acid Atoms Solvent Atoms 575 Heterogen Atoms 172
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing