X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 4.6
Details 0.1 M SODIUM ACETATE PH 4.6, 0.4-1.5 M SODIUM CHLORIDE, 0.00025 M PROTEIN, 0.0027 M LANTHANIDE COMPLEX, 293 K, 3-7 DAYS

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 77.4 α = 90
b = 77.4 β = 90
c = 38.47 γ = 90
Symmetry
Space Group P 43 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD (QUANTUM 315R) ADSC KIRKPATRICK-BAEZ BI-MORPH MIRRORS 2009-05-27
Diffraction Radiation
Monochromator Protocol
CHANNEL CUT CRYOGENICALLY COOLED MONOCHROMATOR CRYSTAL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 -- SOLEIL PROXIMA 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
1.35 19.24 99.7 0.04 -- -- 7.5 -- 26192 -- 3.0 11.16
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)
1.35 1.42 99.2 0.19 -- 3.8 6.8 --

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
SAD 1.35 18.773 -- 1.34 -- 26140 1329 99.59 -- 0.1527 0.1517 0.1719 --
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 1.3499 1.4039 -- 139 2685 0.1892 0.2039 -- 99.0
X Ray Diffraction 1.4039 1.4678 -- 162 2701 0.1617 0.1975 -- 100.0
X Ray Diffraction 1.4678 1.5452 -- 159 2714 0.1467 0.1638 -- 100.0
X Ray Diffraction 1.5452 1.6419 -- 148 2713 0.1387 0.1872 -- 100.0
X Ray Diffraction 1.6419 1.7686 -- 132 2755 0.1409 0.1667 -- 100.0
X Ray Diffraction 1.7686 1.9464 -- 155 2751 0.1379 0.181 -- 100.0
X Ray Diffraction 1.9464 2.2277 -- 152 2766 0.1412 0.163 -- 100.0
X Ray Diffraction 2.2277 2.8051 -- 141 2820 0.1485 0.1469 -- 100.0
X Ray Diffraction 2.8051 18.7748 -- 141 2906 0.1627 0.1808 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 13.17
Anisotropic B[1][1] -0.2538
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.2538
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.5076
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.009
f_chiral_restr 0.114
f_dihedral_angle_d 29.458
f_angle_d 1.815
f_bond_d 0.019
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1000
Nucleic Acid Atoms 0
Heterogen Atoms 90
Solvent Atoms 159

Software

Computing
Computing Package Purpose
XDS, VERSION JANUARY 30, 2009 Data Reduction (intensity integration)
SCALA, VERSION 3.3.16 Data Reduction (data scaling)
SHARP Structure Solution
PHENIX (PHENIX.REFINE) Structure Refinement
Software
Software Name Purpose
PHENIX version: (PHENIX.REFINE) refinement
SHARP model building