3CON

Crystal structure of the human NRAS GTPase bound with GDP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4Q21PDB entry 4Q21

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.529130.0% PEG 3350, 0.2M Magnesium chloride, 0.1 M Tris-HCl, GDP was added to the concentrated protein to a final concentration of 5mM. Crystallization were set up with 1:100 chymotrypsin, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
1.7830.89

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 83.061α = 90
b = 83.061β = 90
c = 38.907γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS2008-03-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E1.5418

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
11.6494099.20.06513.99.718539
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)
1.6491.7192.80.4694.61710

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 4Q211.64935.9671852894999.160.1860.1850.219RANDOM19.437
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]
-0.056-0.028-0.0560.083
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.808
r_dihedral_angle_4_deg14.187
r_dihedral_angle_3_deg11.594
r_dihedral_angle_1_deg5.722
r_scangle_it3.879
r_mcangle_it3.021
r_scbond_it2.846
r_mcbond_it2.396
r_angle_refined_deg1.53
r_angle_other_deg0.943
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.808
r_dihedral_angle_4_deg14.187
r_dihedral_angle_3_deg11.594
r_dihedral_angle_1_deg5.722
r_scangle_it3.879
r_mcangle_it3.021
r_scbond_it2.846
r_mcbond_it2.396
r_angle_refined_deg1.53
r_angle_other_deg0.943
r_mcbond_other0.693
r_symmetry_vdw_other0.26
r_nbd_refined0.211
r_nbd_other0.204
r_nbtor_refined0.176
r_symmetry_vdw_refined0.128
r_symmetry_hbond_refined0.115
r_xyhbond_nbd_refined0.108
r_chiral_restr0.091
r_nbtor_other0.083
r_bond_refined_d0.016
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1216
Nucleic Acid Atoms
Solvent Atoms84
Heterogen Atoms40

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing