2J4Y

Crystal structure of a rhodopsin stabilizing mutant expressed in mammalian cells


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1GZMPDB ENTRY 1GZM

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5VAPOUR DIFFUSION IN SITTING DROPS OF 10-15 MG/ML PROTEIN AND 0.2% C8E4,0.05%LDAO AGAINST 1.1-1.7M LITHIUM SULFATE, 0.1M HEPES PH 7.5
Crystal Properties
Matthews coefficientSolvent content
3.6458

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 109.3α = 90
b = 109.3β = 90
c = 77.7γ = 120
Symmetry
Space GroupP 31

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMICROFOCUSING2004-06-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID13ESRFID13

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
13.45095.90.245.423.0313689-358.2
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.43.584.80.71.792.79

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1GZM3.4501368940795.90.28960.28960.32990.32555.6579
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]
-3.497-7.211-3.4976.994
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d22.40625
c_scangle_it3.81
c_mcangle_it3.13
c_scbond_it2.39
c_mcbond_it1.78
c_angle_deg1.66
c_improper_angle_d1.11414
c_bond_d0.014
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d22.40625
c_scangle_it3.81
c_mcangle_it3.13
c_scbond_it2.39
c_mcbond_it1.78
c_angle_deg1.66
c_improper_angle_d1.11414
c_bond_d0.014
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5184
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms68

Software

Software
Software NamePurpose
CNSrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing