X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.6
Temperature 293.0
Details 0.2M ammonium acetate, 26%(w/v) PEG 4000, 0.1M sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 50.02 α = 90
b = 55.12 β = 104.57
c = 85.96 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 4r -- 2008-11-12
Diffraction Radiation
Monochromator Protocol
Triangular Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON PHOTON FACTORY BEAMLINE BL-6A 0.978 Photon Factory BL-6A

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
2.55 50 99.5 0.099 -- -- 3.6 -- 14870 -- -- 28.14
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)
2.55 2.64 99.9 0.323 -- -- 3.7 1482

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 2.55 37.905 -- 1.34 -- 14854 750 99.06 -- 0.1838 0.1811 0.2338 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 2.5496 2.7464 -- 145 2766 0.226 0.3108 -- 98.0
X Ray Diffraction 2.7464 3.0227 -- 150 2804 0.2172 0.3115 -- 100.0
X Ray Diffraction 3.0227 3.4598 -- 160 2820 0.2029 0.2471 -- 99.0
X Ray Diffraction 3.4598 4.358 -- 139 2824 0.1567 0.2137 -- 99.0
X Ray Diffraction 4.358 37.9088 -- 156 2890 0.1574 0.182 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 32.43
RMS Deviations
Key Refinement Restraint Deviation
f_bond_d 0.003
f_angle_d 0.748
f_chiral_restr 0.05
f_dihedral_angle_d 13.304
f_plane_restr 0.003
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3437
Nucleic Acid Atoms 0
Heterogen Atoms 40
Solvent Atoms 127

Software

Software
Software Name Purpose
SCALEPACK data scaling
PHENIX refinement version: 1.8.2_1309
PDB_EXTRACT data extraction version: 3.15
DENZO data reduction
HKL-2000 data reduction
PHASER phasing