X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 4.6
Temperature 293.0
Details 0.5% PEG4000(w/v), 0.01M sodium acetate, 10mg/ml protein in dark, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 109.79 α = 90
b = 109.79 β = 90
c = 189.11 γ = 120
Symmetry
Space Group P 65

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MAR CCD 165 MM 315 -- 2008-07-21
Diffraction Radiation
Monochromator Protocol
SI(111) DOUBLE-CRYSTAL MONOCHROMATOR SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 14-ID-B -- APS 14-ID-B

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
2.85 50 99.5 0.045 -- -- 7.3 -- 28350 -- 0.0 --
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)
2.85 3.0 99.8 -- -- -- 7.3 --

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
SAD 2.85 42.47 -- 1.34 28493 24940 1281 82.8 -- 0.232 0.229 0.298 --
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 2.85 2.9641 -- 71 1165 0.3437 0.4316 -- 37.0
X Ray Diffraction 2.9641 3.099 -- 71 1698 0.3164 0.3896 -- 54.0
X Ray Diffraction 3.099 3.2623 -- 124 2216 0.2993 0.3513 -- 70.0
X Ray Diffraction 3.2623 3.4666 -- 128 2800 0.2846 0.3897 -- 88.0
X Ray Diffraction 3.4666 3.7341 -- 180 3153 0.2556 0.337 -- 100.0
X Ray Diffraction 3.7341 4.1096 -- 171 3169 0.2392 0.2768 -- 100.0
X Ray Diffraction 4.1096 4.7036 -- 169 3167 0.1938 0.2747 -- 100.0
X Ray Diffraction 4.7036 5.9235 -- 175 3188 0.2069 0.2937 -- 100.0
X Ray Diffraction 5.9235 42.4777 -- 192 3103 0.2005 0.2579 -- 97.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model each chain was treated as an independent TLS group
Anisotropic B[1][1] 7.0301
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 7.0301
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -14.0601
RMS Deviations
Key Refinement Restraint Deviation
f_chiral_restr 0.074
f_plane_restr 0.005
f_dihedral_angle_d 18.014
f_bond_d 0.006
f_angle_d 1.256
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7338
Nucleic Acid Atoms 0
Heterogen Atoms 172
Solvent Atoms 2

Software

Software
Software Name Purpose
BioCARS data collection version: uControl
SHARP phasing
PHENIX refinement version: (phenix.refine)
HKL-2000 data reduction
HKL-2000 data scaling