7O2Y

Sandercyanin Fluorescent Protein variant V71E bound to biliverdin IX-alpha


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5EZ2 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP27711mg/mL 0.2M calcium chloride dihydrate, 20% (w/v) PEG 3350, pH 5.1
Crystal Properties
Matthews coefficientSolvent content
2.1542.91

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 38.466α = 90
b = 38.466β = 90
c = 117.601γ = 90
Symmetry
Space GroupP 41

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 130 mm2013-10-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-20.8729ESRFID23-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
12.538.8499.60.9910.46.841927
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.52.60.306

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-VALUE5EZ22.536.56592029699.70.1770.17320.253536.55
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]
1.0791.079-2.157
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.76
r_dihedral_angle_4_deg19.76
r_dihedral_angle_3_deg18.761
r_lrange_it9.108
r_lrange_other9.088
r_dihedral_angle_1_deg8.435
r_scangle_it5.991
r_scangle_other5.988
r_mcangle_it5.234
r_mcangle_other5.233
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.76
r_dihedral_angle_4_deg19.76
r_dihedral_angle_3_deg18.761
r_lrange_it9.108
r_lrange_other9.088
r_dihedral_angle_1_deg8.435
r_scangle_it5.991
r_scangle_other5.988
r_mcangle_it5.234
r_mcangle_other5.233
r_scbond_it3.775
r_scbond_other3.772
r_mcbond_it3.379
r_mcbond_other3.375
r_angle_refined_deg1.613
r_angle_other_deg1.125
r_xyhbond_nbd_refined0.201
r_symmetry_nbd_other0.19
r_nbd_refined0.189
r_symmetry_xyhbond_nbd_refined0.185
r_nbtor_refined0.163
r_nbd_other0.155
r_symmetry_nbd_refined0.149
r_symmetry_nbtor_other0.078
r_chiral_restr0.066
r_symmetry_xyhbond_nbd_other0.057
r_bond_refined_d0.008
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 Atoms1281
Nucleic Acid Atoms
Solvent Atoms51
Heterogen Atoms43

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing