X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 290.0
Details 25% w/V PEG 4000, 0.2M ammonium formate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 290K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 44.87 α = 90
b = 57.39 β = 90
c = 66.17 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2011-10-05
Diffraction Radiation
Monochromator Protocol
Double crystal, Si(111) MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 8.2.1 0.9799, 0.9801, 0.9428 ALS 8.2.1

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
1.64 50 99.1 0.041 -- -- 4.5 -- n/a -3.0 -3.0 --
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)
1.64 1.67 93.8 0.134 -- -- 3.6 1916

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 1.636 35.348 -- 0.05 21007 21007 1051 96.62 0.1947 0.1947 0.1935 0.2157 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 1.6357 1.7101 -- 111 2121 0.2376 0.289 -- 84.0
X Ray Diffraction 1.7101 1.8003 -- 129 2439 0.207 0.2574 -- 95.0
X Ray Diffraction 1.8003 1.9131 -- 131 2482 0.1852 0.2213 -- 98.0
X Ray Diffraction 1.9131 2.0608 -- 131 2503 0.1752 0.184 -- 98.0
X Ray Diffraction 2.0608 2.2681 -- 134 2533 0.1875 0.2147 -- 99.0
X Ray Diffraction 2.2681 2.5963 -- 135 2585 0.1986 0.2238 -- 100.0
X Ray Diffraction 2.5963 3.2706 -- 137 2591 0.2071 0.2261 -- 100.0
X Ray Diffraction 3.2706 35.3567 -- 143 2702 0.1847 0.1979 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 18.4056
Anisotropic B[1][1] 4.0568
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -3.0854
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.9514
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 15.952
f_plane_restr 0.004
f_chiral_restr 0.075
f_angle_d 1.058
f_bond_d 0.006
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1169
Nucleic Acid Atoms 185
Heterogen Atoms 0
Solvent Atoms 175

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
BnP Structure Solution
PHENIX (phenix.refine: 1.7_650) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
BnP phasing
HKL data reduction