X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 293.0
Details 16% PEG 8,000, 120 mM calcium acetate, 80 mM sodium cacolydate, and 20% glycerol v/v , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 63.23 α = 90
b = 63.23 β = 90
c = 313.76 γ = 120
Symmetry
Space Group P 64 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD -- 2011-06
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH ANOMALOUS
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 23-ID-D 0.9795 APS 23-ID-D

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
2.9 100 97.7 0.097 -- -- 20.3 -- 8865 -- -- --
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)
2.9 2.95 79.7 0.261 -- -- 13.2 345

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
SAD 2.907 48.509 -- 1.34 -- 8763 412 97.31 -- 0.2322 0.2294 0.2864 --
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 2.9074 3.328 -- 129 2567 0.2743 0.3947 -- 93.0
X Ray Diffraction 3.328 4.1926 -- 128 2768 0.2318 0.3336 -- 99.0
X Ray Diffraction 4.1926 48.516 -- 155 3016 0.2167 0.2429 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 75.774
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 22.969
f_plane_restr 0.002
f_chiral_restr 0.05
f_angle_d 0.738
f_bond_d 0.003
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1557
Nucleic Acid Atoms 577
Heterogen Atoms 10
Solvent Atoms 19

Software

Computing
Computing Package Purpose
HKL Data Reduction (intensity integration)
HKL Data Reduction (data scaling)
SOLVE Structure Solution
PHENIX (phenix.refine: 1.8.1_1168) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
RESOLVE density modification
SOLVE phasing
HKL data reduction