X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6
Temperature 293.0
Details 10% MPD (2-methyl-2,4-pentanediol), 40 mM sodium cacodylate pH 6.0, 12 mM spermine tetrahydrochloride, and 80 mM strontium (II) chloride, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 96.15 α = 90
b = 25.89 β = 112.61
c = 69.72 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- --
CCD ADSC QUANTUM 315 -- 2012-04-30
Diffraction Radiation
Monochromator Protocol
-- --
Double crystal, Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 8.2.2 1.0 ALS 8.2.2
SYNCHROTRON ALS BEAMLINE 8.2.1 1.0 ALS 8.2.1

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
1.55 30 95.0 0.039 -- -- 5.9 23564 22386 0.0 -3.0 --
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)
1.55 1.61 69.0 0.039 -- 3.4 2.9 --

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 1.55 30.0 -- -3.0 22350 21233 1153 95.0 -- 0.185 0.182 0.247 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 1.55 1.59 -- 50 1048 0.171 0.258 -- 65.4
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 25.52
Anisotropic B[1][1] 0.39
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.26
Anisotropic B[2][2] 0.75
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.34
RMS Deviations
Key Refinement Restraint Deviation
r_sphericity_bonded 11.255
r_sphericity_free 19.899
r_rigid_bond_restr 5.964
r_gen_planes_refined 0.012
r_chiral_restr 0.085
r_angle_refined_deg 1.526
r_bond_refined_d 0.005
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.124
Luzzati ESD (R-Free Set) 0.104
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 0
Nucleic Acid Atoms 1272
Heterogen Atoms 7
Solvent Atoms 187

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
PHASES Structure Solution
REFMAC 5.6.0117 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.6.0117 refinement
PHASES model building
HKL-2000 data collection