X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8
Temperature 277.0
Details 21% PEG 6000, 180mM calcium acetate, 18% glycerol, 100mM Tris, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 48.59 α = 90
b = 73.88 β = 95.84
c = 178.47 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 -- 2011-04-25
Diffraction Radiation
Monochromator Protocol
Si 511 SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.00 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
2.48 50 99.0 -- -- -- -- 44845 44396 2.0 2.0 --
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)
2.48 2.62 98.3 -- -- 2.35 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 2.481 40.747 -- 1.99 44396 44385 2219 99.0 0.2811 0.2288 0.226 0.2811 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 2.4808 2.5347 -- 137 2614 0.3042 0.3784 -- 98.0
X Ray Diffraction 2.5347 2.5937 -- 139 2632 0.2855 0.3323 -- 99.0
X Ray Diffraction 2.5937 2.6585 -- 135 2573 0.2853 0.3521 -- 99.0
X Ray Diffraction 2.6585 2.7304 -- 138 2614 0.2861 0.3651 -- 99.0
X Ray Diffraction 2.7304 2.8107 -- 137 2609 0.2767 0.3334 -- 99.0
X Ray Diffraction 2.8107 2.9014 -- 138 2617 0.2601 0.3604 -- 99.0
X Ray Diffraction 2.9014 3.0051 -- 138 2629 0.2608 0.327 -- 99.0
X Ray Diffraction 3.0051 3.1253 -- 138 2606 0.2438 0.3291 -- 99.0
X Ray Diffraction 3.1253 3.2675 -- 139 2660 0.2334 0.2975 -- 99.0
X Ray Diffraction 3.2675 3.4397 -- 138 2620 0.2207 0.307 -- 99.0
X Ray Diffraction 3.4397 3.6551 -- 139 2626 0.2167 0.2274 -- 99.0
X Ray Diffraction 3.6551 3.9371 -- 139 2654 0.2001 0.255 -- 99.0
X Ray Diffraction 3.9371 4.3329 -- 140 2655 0.1821 0.2342 -- 99.0
X Ray Diffraction 4.3329 4.9589 -- 140 2658 0.1774 0.2263 -- 99.0
X Ray Diffraction 4.9589 6.2441 -- 140 2666 0.2271 0.2627 -- 99.0
X Ray Diffraction 6.2441 40.7522 -- 144 2733 0.2275 0.2797 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 43.4565
Anisotropic B[1][1] 0.5412
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.1013
Anisotropic B[2][2] -0.5572
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.016
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_dihedral_angle_d 15.786
f_angle_d 1.21
f_bond_d 0.009
f_chiral_restr 0.079
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6991
Nucleic Acid Atoms 0
Heterogen Atoms 60
Solvent Atoms 237

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