X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.5
Temperature 277.0
Details 1.34 M sodium malonate pH 6.0, 0.1 M imidazole maleate pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 96.03 α = 90
b = 37.97 β = 107.38
c = 144.68 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 325 mm CCD -- 2011-12-15
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL9-2 0.9794 SSRL BL9-2

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 48 89.19 0.108 -- -- 5.08 18175 16211 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)
2.48 2.61 75.39 0.37 -- -- 5.29 1959

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 2.4801 34.966 -- 0.0 -- 16049 1271 88.6 -- 0.2393 0.2365 0.2698 --
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 2.4801 2.5793 -- 115 1326 0.2732 0.3416 -- 72.0
X Ray Diffraction 2.5793 2.6967 -- 121 1359 0.2567 0.2809 -- 75.0
X Ray Diffraction 2.6967 2.8388 -- 128 1453 0.2413 0.3171 -- 79.0
X Ray Diffraction 2.8388 3.0165 -- 127 1531 0.2369 0.271 -- 83.0
X Ray Diffraction 3.0165 3.2493 -- 137 1664 0.2482 0.2933 -- 90.0
X Ray Diffraction 3.2493 3.576 -- 153 1785 0.2248 0.2359 -- 97.0
X Ray Diffraction 3.576 4.0928 -- 164 1856 0.2157 0.2438 -- 100.0
X Ray Diffraction 4.0928 5.1538 -- 166 1876 0.2073 0.2555 -- 100.0
X Ray Diffraction 5.1538 34.9694 -- 160 1928 0.2777 0.2988 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 46.2666
Anisotropic B[1][1] 8.843
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.4129
Anisotropic B[2][2] -6.3552
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.4879
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 12.232
f_plane_restr 0.009
f_chiral_restr 0.058
f_angle_d 0.87
f_bond_d 0.012
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2858
Nucleic Acid Atoms 0
Heterogen Atoms 54
Solvent Atoms 72

Software

Computing
Computing Package Purpose
webice Data Collection
MOSFLM Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
Phenix (Phenix.automr: 1.7.1_743 Structure Solution
PHENIX (phenix.refine: 1.7.1_743) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
SCALA version: CCP4_3.2.19 data reduction