2CL7

CRYSTAL STRUCTURE ANALYSIS OF A FLUORESCENT FORM OF H-RAS P21 IN COMPLEX WITH GTP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5P21PDB ENTRY 5P21

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.2291.15PROTEIN SOLUTION: 13.35 MG/ML PROTEIN, 64 MM TRIS PH 7.6, 20 MM MAGNESIUM CHLORIDE, 10 MM DTT, 0,1 MM SODIUM AZIDE; RESERVOIR SOLUTION: 100 MM HEPES PH 7.2, 200 MM MAGNESIUM ACETATE, 16% PEG 8000 (FRESHLY PREPARED) MIXTURE OF EQUAL VOLUMES OF PROTEIN AND RESERVOIR SOLUTION, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291.15K
Crystal Properties
Matthews coefficientSolvent content
2.243.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.28α = 90
b = 69.28β = 90
c = 35.02γ = 90
Symmetry
Space GroupP 41

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2004-12-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-4ESRFID14-4

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
11.2569.3499.90.0420.76.1346204
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)
11.251.399.90.523.55.28

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 5P211.2569.3443911229399.90.1490.1480.17RANDOM8.69
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]
-1.18-1.182.36
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.649
r_dihedral_angle_4_deg17.949
r_dihedral_angle_3_deg14.047
r_dihedral_angle_1_deg6.526
r_scangle_it2.819
r_scbond_it2.064
r_angle_refined_deg1.742
r_mcangle_it1.336
r_mcbond_it1.21
r_angle_other_deg0.806
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.649
r_dihedral_angle_4_deg17.949
r_dihedral_angle_3_deg14.047
r_dihedral_angle_1_deg6.526
r_scangle_it2.819
r_scbond_it2.064
r_angle_refined_deg1.742
r_mcangle_it1.336
r_mcbond_it1.21
r_angle_other_deg0.806
r_symmetry_hbond_refined0.477
r_symmetry_vdw_refined0.384
r_symmetry_vdw_other0.304
r_xyhbond_nbd_refined0.254
r_nbd_refined0.234
r_nbd_other0.188
r_nbtor_refined0.188
r_chiral_restr0.089
r_nbtor_other0.088
r_bond_refined_d0.015
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
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 Atoms208
Heterogen Atoms55

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing