X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 295.0
Details 50 mM MOPS pH 7, 50-200 mM AMMONIUM SULFATE, 50 mM MnCl2, AND 6-9% PEG-3350, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 52.43 α = 90
b = 148.58 β = 90
c = 78.8 γ = 90
Symmetry
Space Group C 2 2 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MAR CCD 165 mm Multilayer mirror, curved to focus in the vertical (R = 400 m) 2009-05-29
Diffraction Radiation
Monochromator Protocol
Bent silicon crystal, horizontally focusing (R = 12 m). Will be planar diamond monochromator. SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON MAX II BEAMLINE I911-5 0.90772 MAX II I911-5

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
1.75 20 99.9 0.094 -- -- 7.3 31515 31474 -- -3.0 25.46
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)
1.75 1.85 99.9 0.65 -- 3.27 7.4 4740

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 1.75 19.7 -- 1.99 -- 31450 945 99.97 -- 0.1481 0.1471 0.1777 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 1.75 1.8422 4388 132 4256 0.2043 0.2699 -- 100.0
X Ray Diffraction 1.8422 1.9576 4470 134 4336 0.1574 0.1712 -- 100.0
X Ray Diffraction 1.9576 2.1085 4440 133 4307 0.1331 0.1726 -- 100.0
X Ray Diffraction 2.1085 2.3204 4476 135 4341 0.1314 0.161 -- 100.0
X Ray Diffraction 2.3204 2.6555 4467 134 4333 0.1379 0.1981 -- 100.0
X Ray Diffraction 2.6555 3.343 4520 136 4384 0.1521 0.1859 -- 100.0
X Ray Diffraction 3.343 19.7012 4689 141 4548 0.1455 0.1591 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic+tls
Mean Isotropic B 21.896
Anisotropic B[1][1] -0.0291
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.0185
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.0105
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 13.784
f_plane_restr 0.011
f_chiral_restr 0.151
f_angle_d 1.884
f_bond_d 0.021
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2276
Nucleic Acid Atoms 0
Heterogen Atoms 48
Solvent Atoms 205

Software

Computing
Computing Package Purpose
MARCCD Data Collection
XDS Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 1.7.1_743) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
phenix refinement
Phaser version: 1.3.3 molecular replacement
Xscale data reduction