X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Hanging Drop
pH 8.5
Temperature 298.0
Details 100mM Tris, pH 8.5, 25% PEG 3350, hanging drop, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 46.7 α = 90
b = 46.7 β = 90
c = 294.1 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2008-07-15
Diffraction Radiation
Monochromator Protocol
Double flat crystal, Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 8.3.1 1.0 ALS 8.3.1

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
2.4 36.6 98.0 0.108 0.118 -- 16.0 13794 13507 2.0 2.0 62.4
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)
2.4 -- 98.0 -- -- -- -- --

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 2.4 36.574 2.0 1.99 13794 13506 1350 97.95 0.221 0.221 0.2157 0.2665 10% 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 2.4 2.4858 -- 131 1182 0.3309 0.3869 -- 97.0
X Ray Diffraction 2.4858 2.5853 -- 130 1170 0.2961 0.3664 -- 98.0
X Ray Diffraction 2.5853 2.7029 -- 128 1153 0.2736 0.3487 -- 97.0
X Ray Diffraction 2.7029 2.8454 -- 131 1186 0.25 0.3387 -- 97.0
X Ray Diffraction 2.8454 3.0236 -- 132 1186 0.2422 0.2791 -- 98.0
X Ray Diffraction 3.0236 3.2569 -- 133 1201 0.2322 0.2786 -- 98.0
X Ray Diffraction 3.2569 3.5844 -- 137 1225 0.2068 0.2899 -- 98.0
X Ray Diffraction 3.5844 4.1025 -- 134 1216 0.1938 0.2125 -- 98.0
X Ray Diffraction 4.1025 5.1664 -- 140 1258 0.1728 0.1885 -- 98.0
X Ray Diffraction 5.1664 36.5785 -- 154 1379 0.2168 0.3005 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 68.6751
Anisotropic B[1][1] 6.3476
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 6.3476
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -12.6953
RMS Deviations
Key Refinement Restraint Deviation
f_bond_d 0.01
f_chiral_restr 0.086
f_angle_d 1.263
f_dihedral_angle_d 16.794
f_plane_restr 0.005
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2369
Nucleic Acid Atoms 0
Heterogen Atoms 30
Solvent Atoms 24

Software

Software
Software Name Purpose
XSCALE data scaling
PHENIX refinement version: dev_613
PDB_EXTRACT data extraction version: 3.10
Blu-Ice data collection
XDS data reduction
PHENIX phasing