8II8

X-ray crystal structure of pink-colored protein from Pleurotus salmoneostramineus in complex with natural chromophore


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherartificial helices without side chain

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP9293PEG4000, sodium formate, Tris-HCl
Crystal Properties
Matthews coefficientSolvent content
2.1141.79

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.879α = 90
b = 31.895β = 95.939
c = 107.416γ = 90
Symmetry
Space GroupI 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2022-07-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL44XU0.9SPring-8BL44XU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.2530.5699.10.0710.0980.0680.999.43.454840
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.251.2798.60.2760.3830.2640.8963.83.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUEartificial helices without side chain1.2530.5654839282698.9780.1330.13110.164114.602
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]
0.6840.017-1.5240.818
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg15.685
r_dihedral_angle_3_deg12.751
r_dihedral_angle_2_deg11.799
r_rigid_bond_restr5.928
r_dihedral_angle_1_deg4.183
r_lrange_it3.566
r_lrange_other3.236
r_scangle_it3.106
r_scangle_other3.105
r_scbond_other2.519
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg15.685
r_dihedral_angle_3_deg12.751
r_dihedral_angle_2_deg11.799
r_rigid_bond_restr5.928
r_dihedral_angle_1_deg4.183
r_lrange_it3.566
r_lrange_other3.236
r_scangle_it3.106
r_scangle_other3.105
r_scbond_other2.519
r_scbond_it2.518
r_angle_refined_deg1.723
r_mcangle_other1.587
r_mcangle_it1.583
r_mcbond_it1.215
r_mcbond_other1.208
r_angle_other_deg0.617
r_nbd_refined0.259
r_nbd_other0.222
r_symmetry_xyhbond_nbd_refined0.192
r_nbtor_refined0.185
r_symmetry_nbd_other0.179
r_symmetry_nbd_refined0.171
r_xyhbond_nbd_refined0.158
r_chiral_restr0.094
r_symmetry_nbtor_other0.07
r_bond_refined_d0.012
r_gen_planes_refined0.01
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1657
Nucleic Acid Atoms
Solvent Atoms312
Heterogen Atoms33

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing