X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 293.0
Details 10mM Tris-HCl, 150mM NaCl, pH 8.0, vapor diffusion, hanging drop, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 39.17 α = 70.08
b = 51.99 β = 80.25
c = 52.18 γ = 78.05
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RAYONIX MX225HE -- 2011-05-21
Diffraction Radiation
Monochromator Protocol
Double-crystal monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.20000 SPRING-8 BL41XU

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
1.95 50 96.2 0.057 -- -- 10.5 26390 26390 0.0 0.0 --
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)
1.95 1.98 78.7 0.27 -- -- 10.4 1082

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 1.95 41.501 -- 1.99 26354 26354 1318 96.04 0.1803 0.1803 0.1782 0.2221 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 1.9501 2.0282 -- 131 2503 0.2202 0.3057 -- 87.0
X Ray Diffraction 2.0282 2.1205 -- 142 2771 0.1962 0.2714 -- 96.0
X Ray Diffraction 2.1205 2.2323 -- 151 2784 0.2035 0.2617 -- 96.0
X Ray Diffraction 2.2323 2.3721 -- 145 2823 0.1875 0.2718 -- 97.0
X Ray Diffraction 2.3721 2.5552 -- 148 2782 0.1828 0.2291 -- 97.0
X Ray Diffraction 2.5552 2.8123 -- 150 2845 0.1799 0.2298 -- 97.0
X Ray Diffraction 2.8123 3.2191 -- 149 2836 0.1896 0.2251 -- 98.0
X Ray Diffraction 3.2191 4.0552 -- 150 2859 0.168 0.2018 -- 99.0
X Ray Diffraction 4.0552 41.5109 -- 152 2833 0.1632 0.1943 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 36.3715
Anisotropic B[1][1] 5.0859
Anisotropic B[1][2] 1.2496
Anisotropic B[1][3] -0.7978
Anisotropic B[2][2] -5.7236
Anisotropic B[2][3] -7.2338
Anisotropic B[3][3] 0.6377
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 16.207
f_plane_restr 0.005
f_chiral_restr 0.078
f_angle_d 1.141
f_bond_d 0.009
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2506
Nucleic Acid Atoms 0
Heterogen Atoms 6
Solvent Atoms 202

Software

Computing
Computing Package Purpose
BSS Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
MOLREP Structure Solution
PHENIX (phenix.refine: 1.7.2_869) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
SCALEPACK data reduction