X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8
Temperature 277.0
Details 0.1M Tris, 0.1M calcium acetate, 20% glycerol, 21% PEG6000, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 48.81 α = 90
b = 73.75 β = 95.86
c = 180.13 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RAYONIX MX225HE -- 2011-06-05
Diffraction Radiation
Monochromator Protocol
Si SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL32XU 1 SPring-8 BL32XU

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
2.75 50 99.4 -- -- -- -- 33487 33286 2.0 2.0 48.02
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)
2.75 2.9 97.7 -- -- 2.15 3.8 --

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
MOLECULAR REPLACEMENT 2.747 40.973 -- 2.0 33286 33280 1665 99.37 0.2649 0.2079 0.2049 0.2649 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 2.7471 2.8279 -- 133 2524 0.3156 0.3881 -- 96.0
X Ray Diffraction 2.8279 2.9191 -- 138 2616 0.2928 0.3804 -- 100.0
X Ray Diffraction 2.9191 3.0234 -- 138 2625 0.2566 0.3388 -- 100.0
X Ray Diffraction 3.0234 3.1444 -- 138 2629 0.2234 0.2888 -- 100.0
X Ray Diffraction 3.1444 3.2875 -- 139 2640 0.2319 0.3024 -- 100.0
X Ray Diffraction 3.2875 3.4607 -- 138 2618 0.2178 0.3026 -- 100.0
X Ray Diffraction 3.4607 3.6774 -- 139 2639 0.2157 0.2957 -- 99.0
X Ray Diffraction 3.6774 3.9612 -- 137 2601 0.2037 0.2516 -- 99.0
X Ray Diffraction 3.9612 4.3594 -- 140 2654 0.1702 0.2337 -- 100.0
X Ray Diffraction 4.3594 4.9892 -- 140 2665 0.1496 0.2093 -- 100.0
X Ray Diffraction 4.9892 6.2823 -- 141 2678 0.2006 0.2447 -- 100.0
X Ray Diffraction 6.2823 40.9771 -- 144 2726 0.1926 0.225 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 49.0961
Anisotropic B[1][1] 14.4211
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -2.1527
Anisotropic B[2][2] -6.0846
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -8.3366
RMS Deviations
Key Refinement Restraint Deviation
f_chiral_restr 0.055
f_angle_d 0.765
f_bond_d 0.003
f_plane_restr 0.003
f_dihedral_angle_d 15.865
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6987
Nucleic Acid Atoms 0
Heterogen Atoms 62
Solvent Atoms 160

Software

Software
Software Name Purpose
ADSC data collection version: Quantum
PHASER phasing
PHENIX refinement version: (phenix.refine: 1.7.3_928)
XDS data reduction
XDS data scaling