X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.99
Temperature 293.0
Details 50mM Sodium cacoldylate, 10mM Barium chloride, 0.5mM Spermine, 30% (v/v) Methyl pentane diol , pH 6.99, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 17.54 α = 90
b = 30.51 β = 90
c = 44.21 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 MARRESEARCH mirrors 2008-09-17
Diffraction Radiation
Monochromator Protocol
mirrors SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE BRUKER AXS MICROSTAR 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
1.67 30 91.9 0.0882 0.0635 -- 4.54 3037 2791 -- -- 26.6
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)
1.67 1.73 89.6 0.2711 0.233 1.7 4.37 183

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 1.67 13.74 -- -- 2427 2427 145 86.05 -- 0.2173 0.21689 0.22312 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 1.673 1.716 12 12 183 0.32 0.245 -- 94.2
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model ISOTROPIC
Mean Isotropic B 16.177
Anisotropic B[1][1] -0.05
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.05
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.0
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 2.583
r_scbond_it 1.925
r_symmetry_hbond_refined 0.214
r_symmetry_vdw_refined 0.167
r_metal_ion_refined 0.4
r_xyhbond_nbd_refined 0.257
r_nbtor_refined 0.274
r_nbd_refined 0.212
r_gen_planes_refined 0.011
r_chiral_restr 0.094
r_angle_refined_deg 2.247
r_bond_refined_d 0.016
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.224
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 0
Nucleic Acid Atoms 240
Heterogen Atoms 1
Solvent Atoms 39

Software

Computing
Computing Package Purpose
MAR345dtb Data Collection
AUTOMAR Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
PHASER Structure Solution
REFMAC 5.2.0019 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.2.0019 refinement
PHASER model building
MAR345dtb data collection