X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 298.0
Details 1.2-1.4 M sodium citrate, 100 mM Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 42.68 α = 90
b = 41.47 β = 104.4
c = 72.65 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 298
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV++ mirror 2010-01-08
Diffraction Radiation
Monochromator Protocol
Rigaku Varimax HR optic SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RUH3R -- -- --

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
1.5 30 89.9 0.086 -- -- 2.1 35975 34955 1.0 2.0 --
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)
1.5 1.55 84.8 0.253 -- -- 2.0 3366

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 1.5 20.737 -- 0.0 35975 34955 1781 88.06 -- 0.1376 0.1361 0.1659 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 1.5 1.5406 -- 135 2259 0.2522 0.2629 -- 79.0
X Ray Diffraction 1.5406 1.5859 -- 126 2363 0.2025 0.249 -- 82.0
X Ray Diffraction 1.5859 1.637 -- 134 2361 0.1683 0.2116 -- 83.0
X Ray Diffraction 1.637 1.6955 -- 129 2465 0.1582 0.2015 -- 85.0
X Ray Diffraction 1.6955 1.7634 -- 137 2475 0.1421 0.2021 -- 86.0
X Ray Diffraction 1.7634 1.8436 -- 133 2509 0.1292 0.1449 -- 88.0
X Ray Diffraction 1.8436 1.9407 -- 119 2602 0.1211 0.1595 -- 89.0
X Ray Diffraction 1.9407 2.0622 -- 137 2610 0.1212 0.1391 -- 90.0
X Ray Diffraction 2.0622 2.2213 -- 143 2625 0.1275 0.152 -- 91.0
X Ray Diffraction 2.2213 2.4445 -- 146 2681 0.1269 0.1674 -- 92.0
X Ray Diffraction 2.4445 2.7975 -- 139 2731 0.1373 0.1667 -- 94.0
X Ray Diffraction 2.7975 3.5217 -- 152 2749 0.1343 0.1665 -- 94.0
X Ray Diffraction 3.5217 20.7395 -- 151 2744 0.1263 0.1453 -- 92.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 23.0573
Anisotropic B[1][1] -0.8443
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.1664
Anisotropic B[2][2] -1.8516
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -3.4649
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.007
f_dihedral_angle_d 13.248
f_bond_d 0.01
f_angle_d 1.272
f_chiral_restr 0.077
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2046
Nucleic Acid Atoms 0
Heterogen Atoms 1
Solvent Atoms 201

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
PHENIX refinement version: 1.7_650
PDB_EXTRACT data extraction version: 3.10
CrystalClear data collection
HKL-2000 data reduction
HKL-2000 data scaling
PHENIX phasing