X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.6
Temperature 291.0
Details EhRho1 at 15 mg/mL in crystallization buffer (50 mM Tris pH 8.0, 250 mM NaCl, 2.5% (v/v) glycerol, 5 mM DTT, 50 microM GTPgammaS, 1 mM magnesium chloride) was mixed 1:1 with and equilibrated against crystallization solution (25% PEG 4000, 150 mM ammonium acetate, 100 mM sodium acetate pH 4.6), VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 36.47 α = 81.75
b = 39.5 β = 80.76
c = 63.58 γ = 65.44
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MAR scanner 300 mm plate custom 2010-11-18
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 22-BM 1.000 APS 22-BM

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
1.8 40 81.6 0.043 -- -- 2.0 29325 23929 0.0 0.0 --
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)
1.8 1.82 45.9 0.278 -- 2.8 1.4 --

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 1.801 32.958 -- 1.96 29486 23882 1214 81.4 -- 0.1744 0.1718 0.2221 --
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 1.801 1.8735 -- 86 1558 0.2154 0.2907 -- 50.0
X Ray Diffraction 1.8735 1.9588 -- 105 1931 0.2029 0.2994 -- 62.0
X Ray Diffraction 1.9588 2.062 -- 126 2250 0.1985 0.2454 -- 73.0
X Ray Diffraction 2.062 2.1912 -- 123 2480 0.1858 0.2512 -- 80.0
X Ray Diffraction 2.1912 2.3603 -- 124 2679 0.1814 0.2339 -- 87.0
X Ray Diffraction 2.3603 2.5978 -- 146 2863 0.1821 0.2334 -- 92.0
X Ray Diffraction 2.5978 2.9735 -- 170 2914 0.1834 0.2413 -- 95.0
X Ray Diffraction 2.9735 3.7454 -- 168 2998 0.1579 0.198 -- 96.0
X Ray Diffraction 3.7454 32.9637 -- 166 2995 0.1527 0.1928 -- 97.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 0.3683
Anisotropic B[1][2] 0.703
Anisotropic B[1][3] -0.5607
Anisotropic B[2][2] -1.8001
Anisotropic B[2][3] 2.6031
Anisotropic B[3][3] 1.4318
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_chiral_restr 0.078
f_dihedral_angle_d 13.895
f_angle_d 1.2
f_bond_d 0.009
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2658
Nucleic Acid Atoms 0
Heterogen Atoms 66
Solvent Atoms 229

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 1.6_289) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.6_289) refinement
PHASER model building
HKL-2000 data collection