X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 289.0
Details 0.1 M SPG buffer, 25% w/v PEG 1500, 10 uM Spermidine, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 47.49 α = 90
b = 147.1 β = 93.68
c = 47.78 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2009-11-11
Diffraction Radiation
Monochromator Protocol
Double crystal, Si(111) or Si(311) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-4 0.9395 ESRF ID14-4

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
2.7 73.55 98.9 -- 0.066 -- 3.4 17783 17783 -- -- --
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)
2.7 2.85 99.7 0.201 0.201 3.8 3.5 2610

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 2.8 45.36 -- 0.0 22705 15885 791 98.71 -- 0.2072 0.2057 0.2367 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 2.8 2.873 -- 42 1106 0.265 0.355 -- 99.83
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 50.88
Anisotropic B[1][1] 0.0
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.01
Anisotropic B[2][2] -0.14
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.13
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 1.897
r_scbond_it 1.146
r_mcangle_it 0.719
r_mcbond_it 0.359
r_gen_planes_refined 0.005
r_chiral_restr 0.067
r_dihedral_angle_4_deg 25.046
r_dihedral_angle_3_deg 16.973
r_dihedral_angle_2_deg 28.486
r_dihedral_angle_1_deg 4.714
r_angle_refined_deg 1.52
r_bond_refined_d 0.009
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2479
Nucleic Acid Atoms 1546
Heterogen Atoms 1
Solvent Atoms 13

Software

Computing
Computing Package Purpose
MXCUBE Data Collection
MOSFLM Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
PHASER Structure Solution
REFMAC 5.5.0110 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
REFMAC5 refinement
Phaser version: 2.1.4 molecular replacement
SCALA version: 3.3.9 data reduction
Mosflm data collection