X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.4
Temperature 293.0
Details pH 4.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Method Vapor Diffusion Hanging Drop
pH 4.4
Temperature 293.0
Details pH 4.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 89.07 α = 90
b = 94.99 β = 90
c = 54.74 γ = 90
Symmetry
Space Group C 2 2 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 95
2 95
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 270 -- 2009-10-14
CCD ADSC QUANTUM 210r -- 2010-01-27
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A -- PHOTON FACTORY AR-NE3A
SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.000 PHOTON FACTORY BL-5A

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 50 99.7 0.031 -- -- 7.2 16110 16062 1.0 1.0 36.36
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)
2.0 2.07 100.0 0.365 -- 4.3 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 2.0 23.747 -- 1.34 -- 16002 801 99.44 -- 0.1892 0.1875 0.2235 --
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 1.9989 2.124 -- 150 2475 0.2332 0.2707 -- 100.0
X Ray Diffraction 2.124 2.2879 -- 139 2493 0.2553 0.3677 -- 99.0
X Ray Diffraction 2.2879 2.5179 -- 148 2500 0.2338 0.2924 -- 100.0
X Ray Diffraction 2.5179 2.8817 -- 125 2545 0.2178 0.2713 -- 100.0
X Ray Diffraction 2.8817 3.6286 -- 117 2566 0.1711 0.2235 -- 100.0
X Ray Diffraction 3.6286 23.7489 -- 122 2622 0.1626 0.1633 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 40.4743
Anisotropic B[1][1] -12.9528
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 10.7675
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 2.1853
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.01
f_chiral_restr 0.119
f_dihedral_angle_d 23.326
f_angle_d 2.071
f_bond_d 0.018
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 525
Nucleic Acid Atoms 570
Heterogen Atoms 36
Solvent Atoms 154

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
SOLVE Structure Solution
PHENIX (phenix.refine: 1.7.3_928) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.6.4_486) refinement
SOLVE model building
HKL-2000 data collection