5EN0

Crystal Structure of T94I rhodopsin mutant


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4A4M 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP277Ammonium sulfate, Sodium acetate

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 242.269α = 90
b = 242.269β = 90
c = 111.147γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2012-02-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA1SLSX06SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.83099.50.110.996115.130386
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.82.9897.60.8440.7221.75.2

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 REPLACEMENTTHROUGHOUT4A4M2.813028815156999.290.209370.207050.25314RANDOM58.989
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]
-2.5-1.25-2.58.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.096
r_dihedral_angle_3_deg16.965
r_dihedral_angle_4_deg13.826
r_long_range_B_refined9.7
r_long_range_B_other9.681
r_scangle_other8.35
r_dihedral_angle_1_deg6.454
r_mcangle_it6.184
r_mcangle_other6.184
r_scbond_it5.594
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.096
r_dihedral_angle_3_deg16.965
r_dihedral_angle_4_deg13.826
r_long_range_B_refined9.7
r_long_range_B_other9.681
r_scangle_other8.35
r_dihedral_angle_1_deg6.454
r_mcangle_it6.184
r_mcangle_other6.184
r_scbond_it5.594
r_scbond_other5.541
r_mcbond_it4.265
r_mcbond_other4.252
r_angle_refined_deg2.118
r_angle_other_deg1.114
r_chiral_restr0.1
r_bond_refined_d0.016
r_gen_planes_refined0.01
r_bond_other_d0.002
r_gen_planes_other0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2701
Nucleic Acid Atoms
Solvent Atoms25
Heterogen Atoms137

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing