X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 293.0
Details 10mM Tris-HCl, 150mM NaCl, 0.2M Na/K tartrate, 8% PEG 3350, pH 8.0, vapor diffusion, hanging drop, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 62.44 α = 90
b = 62.44 β = 90
c = 85.36 γ = 120
Symmetry
Space Group P 31

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 270 -- 2011-07-06
Diffraction Radiation
Monochromator Protocol
Double-crystal monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON PHOTON FACTORY BEAMLINE BL-1A 1 PHOTON FACTORY BL-1A

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
1.98 50 99.8 0.096 -- -- 7.6 25855 25855 0.0 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)
1.98 2.01 98.3 0.479 -- -- 4.4 1293

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 1.981 45.678 -- 2.04 25820 25820 1288 99.68 -- 0.2184 0.2164 0.2549 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 1.9809 2.0602 -- 143 2711 0.3738 0.3938 -- 99.0
X Ray Diffraction 2.0602 2.154 -- 139 2724 0.3248 0.3837 -- 100.0
X Ray Diffraction 2.154 2.2675 -- 144 2729 0.2791 0.3156 -- 100.0
X Ray Diffraction 2.2675 2.4096 -- 143 2727 0.2539 0.2737 -- 100.0
X Ray Diffraction 2.4096 2.5956 -- 142 2740 0.2411 0.2987 -- 100.0
X Ray Diffraction 2.5956 2.8568 -- 145 2732 0.2233 0.2662 -- 100.0
X Ray Diffraction 2.8568 3.2701 -- 148 2714 0.1958 0.2486 -- 100.0
X Ray Diffraction 3.2701 4.1196 -- 143 2736 0.1686 0.1973 -- 100.0
X Ray Diffraction 4.1196 45.6904 -- 141 2719 0.1717 0.2098 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 42.3906
Anisotropic B[1][1] 5.0841
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 5.0841
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -10.1682
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 14.097
f_plane_restr 0.002
f_chiral_restr 0.046
f_angle_d 0.627
f_bond_d 0.012
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2541
Nucleic Acid Atoms 0
Heterogen Atoms 6
Solvent Atoms 184

Software

Computing
Computing Package Purpose
BSS Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
MOLREP Structure Solution
PHENIX (phenix.refine: 1.7.2_869) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
SCALEPACK data reduction