5VIQ

Crystal structure of monomeric near-infrared fluorescent protein miRFP709


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4XTQ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2930.16 M MgCl2, 0.08 M Tris-HCl pH 8.5, 20% w/v PEG 3350, 3.2% 2,2,2-trifluoroethanol
Crystal Properties
Matthews coefficientSolvent content
1.7931.25

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 36.266α = 90
b = 52.86β = 92.7
c = 64.625γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2016-12-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-BM1.0APS22-BM

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
11.3427.5499.60.0550.0650.03315.43.655190
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)
11.341.3997.60.5170.620.3360.8293.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4XTQ1.3427.5453465170199.370.13730.13570.1877RANDOM23.532
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]
1.57-2.43-1.28-0.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.648
r_sphericity_free21.01
r_dihedral_angle_4_deg20.151
r_dihedral_angle_3_deg14.799
r_sphericity_bonded13.257
r_rigid_bond_restr8.78
r_dihedral_angle_1_deg6.78
r_angle_refined_deg2.348
r_angle_other_deg1.509
r_chiral_restr0.136
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.648
r_sphericity_free21.01
r_dihedral_angle_4_deg20.151
r_dihedral_angle_3_deg14.799
r_sphericity_bonded13.257
r_rigid_bond_restr8.78
r_dihedral_angle_1_deg6.78
r_angle_refined_deg2.348
r_angle_other_deg1.509
r_chiral_restr0.136
r_bond_refined_d0.023
r_gen_planes_other0.016
r_gen_planes_refined0.014
r_bond_other_d0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2303
Nucleic Acid Atoms
Solvent Atoms285
Heterogen Atoms43

Software

Software
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
MOLREPphasing