X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5
Temperature 298.0
Details 0.3 M potassium sodium tartrate, 2 M ammonium sulfate, 0.1 m citrate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 92.55 α = 90
b = 92.55 β = 90
c = 167.08 γ = 120
Symmetry
Space Group H 3 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RIGAKU SATURN 944+ Varimax HF 2011-03-12
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.5418 -- --

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
2.6 40 99.7 0.073 -- -- 5.4 -- 8711 -- 1.0 37.0
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)
2.6 2.69 100.0 0.555 -- -- 5.5 860

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 2.601 25.665 -- 0.0 -- 7744 770 88.79 -- 0.1952 0.1891 0.2502 10%
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 2.6012 2.7639 -- 101 880 0.2984 0.349 -- 68.0
X Ray Diffraction 2.7639 2.9771 -- 119 1042 0.2161 0.3186 -- 81.0
X Ray Diffraction 2.9771 3.2761 -- 126 1168 0.172 0.2423 -- 91.0
X Ray Diffraction 3.2761 3.7489 -- 134 1266 0.1682 0.2324 -- 97.0
X Ray Diffraction 3.7489 4.7184 -- 140 1278 0.1462 0.1996 -- 97.0
X Ray Diffraction 4.7184 25.6658 -- 150 1340 0.2247 0.2713 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model isotropic
Mean Isotropic B 48.7466
Anisotropic B[1][1] 8.6633
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 8.6633
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -6.8092
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 17.403
f_plane_restr 0.005
f_chiral_restr 0.064
f_angle_d 1.242
f_bond_d 0.014
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1589
Nucleic Acid Atoms 0
Heterogen Atoms 45
Solvent Atoms 47

Software

Computing
Computing Package Purpose
CrystalClear Data Collection
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 1.7_650) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
phenix refinement
Phaser molecular replacement
SCALEPACK data reduction
DENZO data collection