X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.2
Temperature 291.0
Details 1.0M Na/K phosphate, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 153.66 α = 90
b = 153.66 β = 90
c = 99.28 γ = 120
Symmetry
Space Group H 3

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2010-09-05
Diffraction Radiation
Monochromator Protocol
SAGITALLY FOCUSED Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 1.0000 PHOTON FACTORY BL-17A

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 50 99.0 -- -- -- -- 27113 27025 0.0 0.0 --

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 2.6 21.535 -- 0.08 27025 25400 1278 94.55 0.1985 0.1914 0.189 0.2348 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 2.6001 2.704 -- 122 2366 0.2485 0.3149 -- 82.0
X Ray Diffraction 2.704 2.8268 -- 122 2483 0.2452 0.3081 -- 88.0
X Ray Diffraction 2.8268 2.9755 -- 146 2627 0.248 0.2942 -- 93.0
X Ray Diffraction 2.9755 3.1613 -- 161 2725 0.2308 0.3108 -- 95.0
X Ray Diffraction 3.1613 3.4046 -- 147 2719 0.2152 0.2614 -- 97.0
X Ray Diffraction 3.4046 3.7456 -- 135 2787 0.1871 0.2389 -- 98.0
X Ray Diffraction 3.7456 4.2838 -- 161 2779 0.1556 0.1925 -- 98.0
X Ray Diffraction 4.2838 5.3832 -- 141 2808 0.1316 0.1656 -- 99.0
X Ray Diffraction 5.3832 21.5356 -- 143 2828 0.1711 0.2087 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 38.9057
Anisotropic B[1][1] -1.6239
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.6239
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 3.2478
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 16.588
f_plane_restr 0.005
f_chiral_restr 0.079
f_angle_d 1.223
f_bond_d 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4465
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 134

Software

Computing
Computing Package Purpose
ADSC Quantum Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
PHENIX Structure Solution
PHENIX (phenix.refine: 1.6.1_357) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.6.1_357) refinement
PHENIX model building
ADSC version: Quantum data collection