X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 293.0
Details 9-12% PEG 3350, 0.2 M sodium iodide, 0.1 M Bis-Tris-propane pH 6.5, 0.01 M iron(III) chloride, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 47.91 α = 90
b = 86.53 β = 99.73
c = 55.59 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 315 -- 2009-01-24
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL9-2 1.0 SSRL BL9-2

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
1.95 50 97.2 0.064 -- -- 3.7 -- 31847 -- -- --
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)
1.95 2.02 82.4 0.501 -- -- 2.9 2706

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 1.95 29.048 -- 1.35 -- 31042 1578 94.77 -- 0.2064 0.2037 0.2534 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 1.95 2.0172 -- 123 2255 0.2644 0.3186 -- 72.0
X Ray Diffraction 2.0172 2.098 -- 134 2621 0.2448 0.2958 -- 84.0
X Ray Diffraction 2.098 2.1934 -- 152 2934 0.2411 0.2826 -- 95.0
X Ray Diffraction 2.1934 2.309 -- 141 3048 0.239 0.3313 -- 98.0
X Ray Diffraction 2.309 2.4536 -- 165 3081 0.2226 0.2557 -- 100.0
X Ray Diffraction 2.4536 2.6429 -- 158 3123 0.2153 0.2564 -- 100.0
X Ray Diffraction 2.6429 2.9087 -- 164 3102 0.2182 0.3018 -- 100.0
X Ray Diffraction 2.9087 3.329 -- 181 3079 0.2144 0.272 -- 100.0
X Ray Diffraction 3.329 4.1922 -- 178 3124 0.1651 0.2031 -- 100.0
X Ray Diffraction 4.1922 29.0515 -- 182 3097 0.1786 0.2315 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 36.4093
Anisotropic B[1][1] 3.9374
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -8.4888
Anisotropic B[2][2] -5.9086
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.9712
RMS Deviations
Key Refinement Restraint Deviation
f_chiral_restr 0.072
f_plane_restr 0.006
f_bond_d 0.008
f_angle_d 1.093
f_dihedral_angle_d 16.649
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3412
Nucleic Acid Atoms 0
Heterogen Atoms 47
Solvent Atoms 225

Software

Software
Software Name Purpose
SCALEPACK data scaling
PHENIX refinement version: 1.6.1_336
PDB_EXTRACT data extraction version: 3.10
HKL-2000 data collection
HKL data reduction
PHASER phasing