7AP5

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-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE5NB42.13149.005156062776575.0050.180.17740.22540.685
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
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
r_mcangle_it3.123
r_scbond_it2.639
r_scbond_other2.639
r_mcbond_it2.119
r_mcbond_other2.112
r_angle_refined_deg1.576
r_angle_other_deg1.345
r_nbd_refined0.212
r_nbd_other0.21
r_symmetry_nbd_other0.184
r_symmetry_nbd_refined0.171
r_symmetry_xyhbond_nbd_refined0.161
r_nbtor_refined0.159
r_xyhbond_nbd_refined0.154
r_symmetry_nbtor_other0.09
r_chiral_restr0.077
r_ncsr_local_group_70.062
r_ncsr_local_group_520.062
r_ncsr_local_group_200.061
r_ncsr_local_group_400.061
r_ncsr_local_group_550.061
r_ncsr_local_group_310.06
r_ncsr_local_group_470.059
r_ncsr_local_group_560.055
r_chiral_restr_other0.053
r_ncsr_local_group_250.053
r_ncsr_local_group_440.053
r_ncsr_local_group_500.053
r_ncsr_local_group_540.053
r_ncsr_local_group_140.05
r_ncsr_local_group_410.05
r_ncsr_local_group_490.05
r_ncsr_local_group_260.049
r_ncsr_local_group_530.049
r_ncsr_local_group_220.048
r_ncsr_local_group_430.048
r_ncsr_local_group_360.047
r_ncsr_local_group_420.047
r_ncsr_local_group_100.045
r_ncsr_local_group_130.045
r_ncsr_local_group_210.045
r_ncsr_local_group_230.045
r_ncsr_local_group_240.045
r_ncsr_local_group_480.044
r_ncsr_local_group_350.041
r_ncsr_local_group_120.039
r_ncsr_local_group_510.039
r_ncsr_local_group_90.038
r_ncsr_local_group_160.038
r_ncsr_local_group_320.038
r_ncsr_local_group_330.038
r_ncsr_local_group_180.037
r_ncsr_local_group_50.036
r_ncsr_local_group_80.036
r_ncsr_local_group_110.036
r_ncsr_local_group_390.036
r_ncsr_local_group_10.035
r_ncsr_local_group_60.035
r_ncsr_local_group_170.035
r_ncsr_local_group_270.035
r_ncsr_local_group_290.035
r_ncsr_local_group_300.035
r_ncsr_local_group_380.035
r_ncsr_local_group_30.034
r_ncsr_local_group_150.033
r_ncsr_local_group_190.033
r_ncsr_local_group_280.031
r_ncsr_local_group_340.031
r_ncsr_local_group_450.031
r_ncsr_local_group_460.03
r_ncsr_local_group_20.029
r_ncsr_local_group_40.029
r_ncsr_local_group_370.025
r_symmetry_xyhbond_nbd_other0.019
r_bond_refined_d0.01
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
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