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, VAPOR DIFFUSION, HANGING DROP, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 47.54 α = 90
b = 146.7 β = 93.21
c = 47.79 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 -- 2012-10-31
Diffraction Radiation
Monochromator Protocol
Si(111) double crystal monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 DIAMOND I04

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
3.1 146.81 99.5 0.111 -- -- 3.5 11888 11810 -- -- --
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)
3.1 3.31 99.6 0.666 -- 1.8 3.6 --

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 3.1 34.63 -- -- 11888 11333 548 98.61 -- 0.17194 0.16987 0.21478 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 3.087 3.167 -- 40 753 0.151 0.182 -- 86.29
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 73.261
Anisotropic B[1][1] -0.86
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.27
Anisotropic B[2][2] 1.5
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.64
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_refined 0.008
r_chiral_restr 0.102
r_dihedral_angle_4_deg 20.344
r_dihedral_angle_3_deg 22.384
r_dihedral_angle_2_deg 35.066
r_dihedral_angle_1_deg 7.331
r_angle_refined_deg 1.708
r_bond_refined_d 0.011
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2482
Nucleic Acid Atoms 1546
Heterogen Atoms 0
Solvent Atoms 2

Software

Computing
Computing Package Purpose
GDA Data Collection
MOSFLM Data Reduction (intensity integration)
Aimless Data Reduction (data scaling)
PHASER Structure Solution
REFMAC 5.7.0029 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
REFMAC5 refinement
Phaser version: 2.5.1 molecular replacement
AIMLESS version: 0.1.26 data reduction
Mosflm data collection