X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5.55
Temperature 298.0
Details 0.1 M sodium acetate, pH 5.55, 0.2 M ammonium acetate, 27% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 38.26 α = 90
b = 73.65 β = 90
c = 84.3 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV++ VariMax HF 2011-02-01
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418 -- --

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
1.8 18.55 98.2 -- 0.036 -- 4.7 22258 22258 1.0 1.0 30.207
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)
1.8 1.9 97.2 0.488 0.488 1.6 4.5 3171

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 1.8 18.553 -- 1.36 22299 22258 1134 97.84 -- 0.2028 0.201 0.2377 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 1.8001 1.8819 -- 154 2547 0.3461 0.3862 -- 97.0
X Ray Diffraction 1.8819 1.981 -- 139 2559 0.2548 0.3272 -- 97.0
X Ray Diffraction 1.981 2.105 -- 134 2637 0.203 0.2048 -- 98.0
X Ray Diffraction 2.105 2.2672 -- 142 2664 0.1907 0.2554 -- 100.0
X Ray Diffraction 2.2672 2.4949 -- 133 2659 0.2064 0.225 -- 99.0
X Ray Diffraction 2.4949 2.8548 -- 141 2646 0.2148 0.2921 -- 98.0
X Ray Diffraction 2.8548 3.5925 -- 146 2642 0.2026 0.2562 -- 97.0
X Ray Diffraction 3.5925 18.5539 -- 145 2770 0.1792 0.1935 -- 96.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Anisotropic
Mean Isotropic B 42.702
Anisotropic B[1][1] -0.4851
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.0196
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.4655
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 15.77
f_plane_restr 0.006
f_chiral_restr 0.103
f_angle_d 1.343
f_bond_d 0.011
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1850
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 86

Software

Computing
Computing Package Purpose
CrystalClear Data Collection
MOSFLM Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 1.7.3_928) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
DM version: 6.2 density modification
Phaser version: 2.3.0 molecular replacement
SCALA version: 3.3.20 data reduction
Mosflm version: 3.3.20 data collection