5B30

H-Ras WT in complex with GppNHp (state 1) after structural transition by humidity control


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3K8Y 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.5293PEG400, SODIUM ACETATE, CALCIUM ACETATE, MAGNESIUM CHLORIDE
Crystal Properties
Matthews coefficientSolvent content
2.5551.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.791α = 90
b = 91.791β = 90
c = 121.417γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2012-10-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL38B11.0SPring-8BL38B1

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
11.6301000.0594910.626298
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)
11.61.631000.8233.8

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 REPLACEMENTTHROUGHOUT3K8Y1.628.3624764132899.310.168140.166670.19569RANDOM23.268
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]
0.020.010.02-0.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.311
r_dihedral_angle_4_deg19.508
r_dihedral_angle_3_deg14.116
r_long_range_B_refined7.06
r_long_range_B_other6.848
r_dihedral_angle_1_deg6.034
r_scangle_other5.259
r_scbond_it3.623
r_scbond_other3.56
r_mcangle_other3.426
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.311
r_dihedral_angle_4_deg19.508
r_dihedral_angle_3_deg14.116
r_long_range_B_refined7.06
r_long_range_B_other6.848
r_dihedral_angle_1_deg6.034
r_scangle_other5.259
r_scbond_it3.623
r_scbond_other3.56
r_mcangle_other3.426
r_mcangle_it3.421
r_mcbond_it2.515
r_angle_refined_deg2.404
r_mcbond_other2.354
r_angle_other_deg1.191
r_chiral_restr0.158
r_bond_refined_d0.027
r_gen_planes_refined0.013
r_gen_planes_other0.003
r_bond_other_d0.002
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 Atoms1317
Nucleic Acid Atoms
Solvent Atoms163
Heterogen Atoms36

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing