X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 293.0
Details PEG 8000, sodium cacodylate, pH 6.5, vapor diffusion, hanging drop, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 48 α = 90
b = 78.58 β = 106.13
c = 85.89 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Detector
Detector Diffraction Type Details Collection Date
-- -- -- 2011-02-17
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID23-1 0.976300 ESRF ID23-1

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 36.53 96.3 0.099 -- -- 3.3 54388 54388 -- -- --
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 1.9 96.3 -- -- -- -- --

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 1.8 28.451 -- 1.34 -- 54339 5457 95.62 -- 0.2088 0.2066 0.2284 --
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 1.8 1.8205 -- 186 1636 0.2276 0.2835 -- 96.0
X Ray Diffraction 1.8205 1.8419 -- 176 1631 0.2155 0.2511 -- 96.0
X Ray Diffraction 1.8419 1.8643 -- 168 1624 0.2187 0.2423 -- 96.0
X Ray Diffraction 1.8643 1.8879 -- 170 1622 0.2158 0.2485 -- 96.0
X Ray Diffraction 1.8879 1.9128 -- 192 1676 0.2251 0.255 -- 97.0
X Ray Diffraction 1.9128 1.939 -- 193 1579 0.2095 0.2643 -- 96.0
X Ray Diffraction 1.939 1.9667 -- 181 1640 0.2125 0.2799 -- 96.0
X Ray Diffraction 1.9667 1.996 -- 175 1659 0.2158 0.2554 -- 97.0
X Ray Diffraction 1.996 2.0272 -- 211 1571 0.2322 0.2431 -- 97.0
X Ray Diffraction 2.0272 2.0604 -- 185 1654 0.2214 0.2594 -- 97.0
X Ray Diffraction 2.0604 2.0959 -- 194 1665 0.2325 0.2692 -- 97.0
X Ray Diffraction 2.0959 2.134 -- 175 1617 0.2218 0.2452 -- 97.0
X Ray Diffraction 2.134 2.1751 -- 180 1690 0.218 0.2345 -- 97.0
X Ray Diffraction 2.1751 2.2195 -- 196 1595 0.2097 0.2293 -- 97.0
X Ray Diffraction 2.2195 2.2677 -- 176 1670 0.2053 0.2416 -- 97.0
X Ray Diffraction 2.2677 2.3204 -- 194 1648 0.2151 0.233 -- 97.0
X Ray Diffraction 2.3204 2.3784 -- 176 1669 0.2102 0.2168 -- 97.0
X Ray Diffraction 2.3784 2.4427 -- 170 1621 0.2119 0.2377 -- 97.0
X Ray Diffraction 2.4427 2.5145 -- 210 1645 0.2179 0.25 -- 97.0
X Ray Diffraction 2.5145 2.5956 -- 186 1652 0.2196 0.2656 -- 97.0
X Ray Diffraction 2.5956 2.6884 -- 174 1667 0.2191 0.248 -- 97.0
X Ray Diffraction 2.6884 2.7959 -- 165 1649 0.2274 0.2335 -- 97.0
X Ray Diffraction 2.7959 2.923 -- 162 1647 0.2116 0.2087 -- 96.0
X Ray Diffraction 2.923 3.077 -- 173 1655 0.213 0.2417 -- 96.0
X Ray Diffraction 3.077 3.2695 -- 196 1618 0.2182 0.2338 -- 95.0
X Ray Diffraction 3.2695 3.5215 -- 198 1604 0.211 0.233 -- 94.0
X Ray Diffraction 3.5215 3.8751 -- 187 1622 0.1862 0.2096 -- 95.0
X Ray Diffraction 3.8751 4.434 -- 176 1605 0.1631 0.1835 -- 93.0
X Ray Diffraction 4.434 5.5795 -- 175 1596 0.1647 0.1587 -- 92.0
X Ray Diffraction 5.5795 28.4549 -- 157 1455 0.1879 0.1797 -- 82.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 0.3479
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 1.4876
Anisotropic B[2][2] -3.75
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.3924
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.006
f_chiral_restr 0.096
f_dihedral_angle_d 16.135
f_angle_d 1.222
f_bond_d 0.01
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4708
Nucleic Acid Atoms 0
Heterogen Atoms 2
Solvent Atoms 236

Software

Computing
Computing Package Purpose
MOSFLM Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 1.7.3_928) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
Phaser molecular replacement
SCALA data reduction
Mosflm data collection