6YBY

Crystal structure of the D116N mutant of the light-driven sodium pump KR2 in the monomeric form, pH 4.6


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1LIPIDIC CUBIC PHASE4.62932 M NaMal pH 4.6
Crystal Properties
Matthews coefficientSolvent content
3.2361.95

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 40.887α = 90
b = 83.601β = 90
c = 233.83γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2018-08-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID30B0.978ESRFID30B

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
11.840.8199.80.0460.050.020.99916.26.637771
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)
11.81.8499.711.0810.4060.9057

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 REPLACEMENTTHROUGHOUT4xtl1.819.8335822192199.650.20230.20130.22RANDOM43.739
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]
0.250.41-0.66
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.118
r_dihedral_angle_4_deg27.804
r_dihedral_angle_3_deg12.954
r_dihedral_angle_1_deg4.729
r_angle_other_deg1.097
r_angle_refined_deg1.068
r_chiral_restr0.053
r_gen_planes_refined0.004
r_bond_refined_d0.003
r_bond_other_d
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.118
r_dihedral_angle_4_deg27.804
r_dihedral_angle_3_deg12.954
r_dihedral_angle_1_deg4.729
r_angle_other_deg1.097
r_angle_refined_deg1.068
r_chiral_restr0.053
r_gen_planes_refined0.004
r_bond_refined_d0.003
r_bond_other_d
r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2147
Nucleic Acid Atoms
Solvent Atoms152
Heterogen Atoms269

Software

Software
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing