X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
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 GDP, 1 mM magnesium chloride) was mixed 1:1 with and equilibrated against crystallization solution (1.5 M ammonium sulfate, 100 mM Tris pH 8.0), VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 50.3 α = 90
b = 54.48 β = 90
c = 132.29 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MAR scanner 300 mm plate custom 2010-11-05
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 22-ID 1.000 APS 22-ID

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
1.95 28.32 99.4 0.047 -- -- 2.5 27432 27267 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)
1.95 1.98 99.4 0.187 -- 2.5 1.7 --

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 1.95 28.324 -- 0.12 27432 27158 1366 99.58 -- 0.1586 0.1565 0.1974 --
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 1.95 2.0194 -- 123 2537 0.1897 0.2585 -- 99.0
X Ray Diffraction 2.0194 2.1002 -- 124 2545 0.164 0.2257 -- 100.0
X Ray Diffraction 2.1002 2.1958 -- 123 2539 0.1554 0.2303 -- 100.0
X Ray Diffraction 2.1958 2.3115 -- 132 2542 0.1514 0.2048 -- 99.0
X Ray Diffraction 2.3115 2.4562 -- 128 2551 0.1533 0.2424 -- 100.0
X Ray Diffraction 2.4562 2.6458 -- 146 2569 0.1632 0.2075 -- 100.0
X Ray Diffraction 2.6458 2.9118 -- 132 2562 0.1723 0.2205 -- 100.0
X Ray Diffraction 2.9118 3.3325 -- 146 2586 0.1733 0.2467 -- 100.0
X Ray Diffraction 3.3325 4.1965 -- 142 2635 0.1411 0.1663 -- 100.0
X Ray Diffraction 4.1965 28.3267 -- 170 2726 0.1412 0.1536 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] -0.0786
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.1266
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.048
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.006
f_chiral_restr 0.088
f_dihedral_angle_d 16.0
f_angle_d 1.26
f_bond_d 0.009
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2759
Nucleic Acid Atoms 0
Heterogen Atoms 73
Solvent Atoms 213

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