X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 4.5
Temperature 293.0
Details 4-10 % (w/v) PEG 400 15-25 mM Zinc acetate 100 mM Sodium acetate, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 110.07 α = 90
b = 110.07 β = 90
c = 82.82 γ = 90
Symmetry
Space Group P 41

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL PSI PILATUS 6M -- 2012-01-08
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL11-1 1.03325 SSRL BL11-1

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
3.25 28.64 97.7 -- 0.064 -- 2.3 -- 29898 -- -- --
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)
3.25 3.3 98.7 -- 0.582 2.0 2.4 --

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
MIRAS 3.25 28.64 -- 1.11 30618 29898 1499 97.77 -- 0.2051 0.2035 0.2345 --
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 3.2502 3.3549 -- 134 2629 0.3058 0.305 -- 99.0
X Ray Diffraction 3.3549 3.4746 -- 144 2560 0.2685 0.3085 -- 98.0
X Ray Diffraction 3.4746 3.6135 -- 128 2665 0.2513 0.3442 -- 98.0
X Ray Diffraction 3.6135 3.7776 -- 170 2520 0.2399 0.3198 -- 98.0
X Ray Diffraction 3.7776 3.9763 -- 149 2554 0.22 0.2688 -- 97.0
X Ray Diffraction 3.9763 4.2247 -- 143 2550 0.1982 0.2096 -- 98.0
X Ray Diffraction 4.2247 4.5497 -- 111 2629 0.1733 0.2413 -- 98.0
X Ray Diffraction 4.5497 5.0054 -- 133 2568 0.1757 0.2096 -- 98.0
X Ray Diffraction 5.0054 5.7246 -- 137 2588 0.1927 0.1948 -- 98.0
X Ray Diffraction 5.7246 7.1935 -- 83 2619 0.1881 0.2375 -- 98.0
X Ray Diffraction 7.1935 28.6451 -- 167 2517 0.1874 0.1918 -- 96.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 6.1583
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 6.1583
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -12.3166
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.003
f_chiral_restr 0.267
f_dihedral_angle_d 22.458
f_angle_d 0.88
f_bond_d 0.005
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3189
Nucleic Acid Atoms 0
Heterogen Atoms 145
Solvent Atoms 0

Software

Computing
Computing Package Purpose
BLU-ICE Data Collection
XDS Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
SHARP Structure Solution
PHENIX (phenix.refine: 1.7.3_928) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.7.3_928) refinement
SHARP model building
BLU-ICE data collection