3SEA

Structure of Rheb-Y35A mutant in GDP- and GMPPNP-bound forms


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.5
Temperature 293.0
Details 100 mM Tris hydrochloride, 200 mM Sodium acetate trihydrate, 30% w/v Polyethylene glycol 4,000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 57.25 α = 90
b = 69.87 β = 90
c = 79.19 γ = 90
Symmetry
Space Group P 2 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RUH3R 1.54 -- --

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot
2 50 99.8 0.093 0.093 -- 7.0 -- 21742 0.0 3.0 --
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
2.0 2.03 100.0 0.412 0.412 4.597 6.6 --

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
MOLECULAR REPLACEMENT 2.0 26.919 -- 0.0 -- 21742 1961 98.19 -- 0.1665 0.1618 0.214 --
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 2.0 2.0697 -- 183 1876 0.1684 0.2492 -- 95.0
X Ray Diffraction 2.0697 2.1526 -- 191 1907 0.163 0.2391 -- 97.0
X Ray Diffraction 2.1526 2.2505 -- 190 1947 0.1628 0.2585 -- 98.0
X Ray Diffraction 2.2505 2.3691 -- 191 1932 0.1651 0.2242 -- 97.0
X Ray Diffraction 2.3691 2.5174 -- 198 1965 0.1589 0.2357 -- 98.0
X Ray Diffraction 2.5174 2.7116 -- 196 1966 0.1666 0.251 -- 99.0
X Ray Diffraction 2.7116 2.9842 -- 199 2007 0.17 0.2199 -- 100.0
X Ray Diffraction 2.9842 3.4153 -- 198 2007 0.1724 0.2295 -- 100.0
X Ray Diffraction 3.4153 4.3 -- 203 2040 0.1477 0.1862 -- 100.0
X Ray Diffraction 4.3 26.9216 -- 212 2134 0.1602 0.1773 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 6.1797
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.3176
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -5.8621
RMS Deviations
Key Refinement Restraint Deviation
f_bond_d 0.007
f_chiral_restr 0.075
f_angle_d 1.141
f_plane_restr 0.004
f_dihedral_angle_d 16.599
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2640
Nucleic Acid Atoms 0
Heterogen Atoms 66
Solvent Atoms 252

Software

Software
Software Name Purpose
CrystalClear data collection
PHENIX model building
PHENIX refinement version: (phenix.refine: 1.6.4_486)
HKL-2000 data reduction
HKL-2000 data scaling
PHENIX phasing