6YX7

The high resolution structure of allophycocyanin from cyanobacterium Nostoc sp. WR13, the P21212 crystal form.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1B33 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5293Morpheus screen condition H12: Precipitant mix 4: 25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350; Buffer system 3: 1.0M Tris (base); bicine, pH 8.5 Additives: amino acids: 0.2M Gly, DL-Ala, DL-Ser, DL-Glu, DL-Lys
Crystal Properties
Matthews coefficientSolvent content
2.9558.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 123.695α = 90
b = 177.726β = 90
c = 106.372γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2018-07-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.97932DiamondI03

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
11.419106.37296.10.0770.0820.0270.99813.88.738304719.64
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)
11.4191.50361.31.221.3130.4780.6231.77.2

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-VALUE1B331.419106.3723830471913387.2580.1280.12550.175125.715
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]
1.042.665-3.705
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.912
r_dihedral_angle_other_3_deg30.531
r_dihedral_angle_4_deg15.71
r_dihedral_angle_3_deg13.745
r_lrange_it5.396
r_dihedral_angle_1_deg4.856
r_lrange_other4.683
r_scangle_it3.961
r_scangle_other3.961
r_scbond_it3.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.912
r_dihedral_angle_other_3_deg30.531
r_dihedral_angle_4_deg15.71
r_dihedral_angle_3_deg13.745
r_lrange_it5.396
r_dihedral_angle_1_deg4.856
r_lrange_other4.683
r_scangle_it3.961
r_scangle_other3.961
r_scbond_it3.3
r_scbond_other3.3
r_mcangle_it2.914
r_mcangle_other2.914
r_rigid_bond_restr2.503
r_mcbond_it2.392
r_mcbond_other2.392
r_angle_refined_deg1.517
r_angle_other_deg1.489
r_symmetry_nbd_refined0.262
r_nbd_refined0.218
r_nbd_other0.214
r_symmetry_xyhbond_nbd_refined0.196
r_symmetry_nbd_other0.182
r_xyhbond_nbd_refined0.171
r_nbtor_refined0.169
r_symmetry_xyhbond_nbd_other0.123
r_ncsr_local_group_260.113
r_ncsr_local_group_30.111
r_ncsr_local_group_40.11
r_ncsr_local_group_140.108
r_ncsr_local_group_290.108
r_ncsr_local_group_130.106
r_ncsr_local_group_210.104
r_ncsr_local_group_190.103
r_ncsr_local_group_180.102
r_ncsr_local_group_250.102
r_ncsr_local_group_170.098
r_ncsr_local_group_150.097
r_ncsr_local_group_20.096
r_ncsr_local_group_280.096
r_ncsr_local_group_110.095
r_ncsr_local_group_60.094
r_ncsr_local_group_200.094
r_ncsr_local_group_270.094
r_ncsr_local_group_50.093
r_ncsr_local_group_120.093
r_ncsr_local_group_10.092
r_ncsr_local_group_80.09
r_ncsr_local_group_70.089
r_ncsr_local_group_90.087
r_ncsr_local_group_160.087
r_ncsr_local_group_300.087
r_chiral_restr0.084
r_ncsr_local_group_240.084
r_symmetry_nbtor_other0.083
r_ncsr_local_group_220.08
r_ncsr_local_group_100.075
r_ncsr_local_group_230.064
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_bond_other_d0.003
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms14448
Nucleic Acid Atoms
Solvent Atoms3208
Heterogen Atoms841

Software

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