X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.6
Temperature 298.0
Details 100mM sodium acetate trihydrate, 0.2M ammonium sulfate, 25% PEG 4000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Method Vapor Diffusion Hanging Drop
pH 6.9
Temperature 298.0
Details 0.49M sodium phosphate monobasic monohydrate - 0.91M potassium phosphate dibasic, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 51.76 α = 90
b = 51.76 β = 90
c = 91.56 γ = 90
Symmetry
Space Group I 4 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
2 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RAYONIX MX-300 -- 2011-10-06
CCD ADSC QUANTUM 315r -- 2011-09-08
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Si(111) MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON CLSI BEAMLINE 08ID-1 0.9795 CLSI 08ID-1
SYNCHROTRON ALS BEAMLINE 12.3.1 0.9793, 1.116 ALS 12.3.1

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 45.06 98.6 0.032 -- -- -- 25782 25782 -3.0 -3.0 21.595
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 1.39 98.5 0.481 -- 2.07 -- --

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
MAD 1.35 45.058 -- -3.0 14001 14001 704 99.41 -- 0.1629 0.1618 0.182 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 1.3501 1.4543 -- 137 2600 0.2032 0.3067 -- 100.0
X Ray Diffraction 1.4543 1.6007 -- 138 2625 0.1529 0.2135 -- 100.0
X Ray Diffraction 1.6007 1.8323 -- 141 2662 0.1452 0.188 -- 100.0
X Ray Diffraction 1.8323 2.3085 -- 140 2657 0.1355 0.1654 -- 100.0
X Ray Diffraction 2.3085 45.0836 -- 148 2753 0.1735 0.1697 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 21.7243
Anisotropic B[1][1] -1.1799
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.1799
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 2.3598
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 16.056
f_plane_restr 0.007
f_chiral_restr 0.091
f_angle_d 1.437
f_bond_d 0.014
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 522
Nucleic Acid Atoms 0
Heterogen Atoms 4
Solvent Atoms 66

Software

Computing
Computing Package Purpose
MxDC Data Collection
XDS Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
PHENIX (1.7.3_928) Structure Solution
PHENIX (phenix.refine: 1.7.3_928) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
Xscale data reduction