7AP5 | pdb_00007ap5

Crystal structure of phycoerythrin from cyanobacterium Nostoc sp. WR13 contains multiple stacks of hexameric assemblies which resemble the rods of phycobilisome.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5NB4 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP294.15Morpheus screen condition C9: 10% w/v PEG 20 000, 20% v/v PEG MME 550 precipitants; 0.03 M NPS (Nitrate, Phosphate & Sulfate) mix of additives; 0.01 M bicine/Trizma base pH 8.5 buffer system
Crystal Properties
Matthews coefficientSolvent content
2.9458.09

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 192.759α = 90
b = 192.759β = 90
c = 524.486γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2018-09-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.97950DiamondI04

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
12.13159.0795.60.2830.2980.0930.996810.215606729.7
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)
12.1332.32280.11.6531.7490.5670.6221.69.3

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)Mean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE5NB42.13149.005156062776575.0050.180.17740.190.2250.2340.685
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]
-0.09-0.045-0.090.291
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.412
r_dihedral_angle_4_deg18.323
r_dihedral_angle_3_deg14.236
r_dihedral_angle_other_3_deg9.212
r_lrange_it6.056
r_lrange_other6.013
r_dihedral_angle_1_deg5.33
r_scangle_other4.066
r_scangle_it4.064
r_mcangle_other3.125
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms20592
Nucleic Acid Atoms
Solvent Atoms1365
Heterogen Atoms4153

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata processing
pointlessdata scaling
Aimlessdata scaling
STARANISOdata scaling
PHASERphasing
XDSdata reduction