X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 293.0
Details 1.6M Sodium Citrate. 50mM Tris-Cl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 42.23 α = 90
b = 41.12 β = 104.39
c = 71.9 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV++ -- 2010-07-13
Diffraction Radiation
Monochromator Protocol
VARIMAX OPTICS SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RUH3R 1.5418 -- --

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
1.49 50 97.8 0.064 -- -- 4.3 39387 38521 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)
1.49 1.54 91.7 0.397 -- -- 4.0 3578

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 1.49 23.761 -- 0.0 39387 37666 1877 95.75 -- 0.151 0.15 0.1712 RANDOM
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 1.49 1.543 -- 175 3126 0.391 0.4154 -- 85.0
X Ray Diffraction 1.543 1.6048 -- 170 3422 0.2578 0.2662 -- 92.0
X Ray Diffraction 1.6048 1.6778 -- 195 3470 0.1909 0.226 -- 94.0
X Ray Diffraction 1.6778 1.7663 -- 174 3546 0.1499 0.1663 -- 95.0
X Ray Diffraction 1.7663 1.8769 -- 187 3591 0.1304 0.1866 -- 97.0
X Ray Diffraction 1.8769 2.0217 -- 189 3665 0.1345 0.1845 -- 98.0
X Ray Diffraction 2.0217 2.2251 -- 200 3678 0.1406 0.1649 -- 99.0
X Ray Diffraction 2.2251 2.5467 -- 196 3702 0.1355 0.1638 -- 99.0
X Ray Diffraction 2.5467 3.2073 -- 194 3752 0.1383 0.1565 -- 100.0
X Ray Diffraction 3.2073 23.764 -- 197 3837 0.1455 0.1482 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 20.8308
Anisotropic B[1][1] -0.0637
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 1.0708
Anisotropic B[2][2] -1.7736
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.8374
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.008
f_bond_d 0.013
f_angle_d 1.532
f_chiral_restr 0.092
f_dihedral_angle_d 13.928
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2049
Nucleic Acid Atoms 0
Heterogen Atoms 13
Solvent Atoms 290

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
PHENIX refinement version: 1.6.3_467
PDB_EXTRACT data extraction version: 3.10
CrystalClear data collection
PHENIX phasing