6RFA

Crystal structure of the H30K mutant of the light-driven sodium pump KR2 in the monomeric form, pH 8.0


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1LIPIDIC CUBIC PHASE2932.0 M Sodium Malonate, pH 8.0
Crystal Properties
Matthews coefficientSolvent content
3.2962.62

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 40.738α = 90
b = 84.178β = 90
c = 234.541γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2015-11-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE MASSIF-20.968ESRFMASSIF-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
12.242.0999.90.9977.45.421097
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)
12.22.270.4761

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 REPLACEMENTTHROUGHOUT4XTL2.219.8920046101399.620.21070.20930.2377RANDOM39.81
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]
-0.140.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.102
r_dihedral_angle_4_deg19.814
r_dihedral_angle_3_deg16.388
r_dihedral_angle_1_deg7.438
r_angle_other_deg0.758
r_angle_refined_deg0.729
r_chiral_restr0.042
r_bond_refined_d0.004
r_gen_planes_refined0.003
r_bond_other_d
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.102
r_dihedral_angle_4_deg19.814
r_dihedral_angle_3_deg16.388
r_dihedral_angle_1_deg7.438
r_angle_other_deg0.758
r_angle_refined_deg0.729
r_chiral_restr0.042
r_bond_refined_d0.004
r_gen_planes_refined0.003
r_bond_other_d
r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2131
Nucleic Acid Atoms
Solvent Atoms38
Heterogen Atoms290

Software

Software
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing