6YX8

The structure of allophycocyanin from cyanobacterium Nostoc sp. WR13, the C2221 crystal form.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6YX7 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5293Morpheus screen condition E12: 37.5% v/v Precipitant mix 4: 25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350; 0.1M Buffer system 3: 1.0M Tris (base); bicine, pH 8.5 0.12M Additives: 0.3M ethylene glycols
Crystal Properties
Matthews coefficientSolvent content
2.6653.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 104.676α = 90
b = 177.34β = 90
c = 122.416γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2018-09-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.91587DiamondI04-1

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
11.83190.14495.70.1260.1370.0530.9969.36.68724926.15
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)
11.8311.94158.31.2781.2780.5240.5991.5

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-VALUE6YX71.83190.14487257433987.2650.1610.15950.198332.791
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]
0.262-0.4520.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.274
r_dihedral_angle_4_deg18.567
r_dihedral_angle_3_deg14.545
r_dihedral_angle_other_3_deg13.127
r_lrange_it6.711
r_lrange_other6.338
r_dihedral_angle_1_deg5.18
r_scangle_it4.005
r_scangle_other4.005
r_mcangle_other2.558
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.274
r_dihedral_angle_4_deg18.567
r_dihedral_angle_3_deg14.545
r_dihedral_angle_other_3_deg13.127
r_lrange_it6.711
r_lrange_other6.338
r_dihedral_angle_1_deg5.18
r_scangle_it4.005
r_scangle_other4.005
r_mcangle_other2.558
r_mcangle_it2.556
r_scbond_it2.521
r_scbond_other2.521
r_mcbond_it1.749
r_mcbond_other1.745
r_angle_refined_deg1.547
r_angle_other_deg1.351
r_nbd_other0.255
r_symmetry_xyhbond_nbd_refined0.255
r_symmetry_nbd_refined0.239
r_xyhbond_nbd_other0.224
r_nbd_refined0.213
r_xyhbond_nbd_refined0.208
r_symmetry_nbd_other0.182
r_nbtor_refined0.162
r_symmetry_xyhbond_nbd_other0.135
r_ncsr_local_group_60.111
r_ncsr_local_group_50.102
r_ncsr_local_group_10.099
r_ncsr_local_group_40.096
r_ncsr_local_group_20.095
r_ncsr_local_group_30.092
r_symmetry_nbtor_other0.086
r_chiral_restr0.083
r_bond_refined_d0.01
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7224
Nucleic Acid Atoms
Solvent Atoms928
Heterogen Atoms936

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
autoPROCdata scaling
STARANISOdata scaling
PHASERphasing
Cootmodel building