X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 298.0
Details 100mM HEPES, 200mM MgCl2, 30% PEG 400, 2mM ATP, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 43.69 α = 90
b = 71.56 β = 90
c = 118.61 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 130
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 6M -- 2012-03-18
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X25 1.10 NSLS X25

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
2.1 45.6 98.9 -- -- -- -- 22461 22214 -- -3.0 --
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)
2.1 2.21 92.9 -- -- -- -- --

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 2.1 35.78 -- 1.35 22414 22154 1740 98.84 -- 0.181 0.1769 0.2282 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 2.1 2.1618 -- 121 1505 0.2091 0.2748 -- 89.0
X Ray Diffraction 2.1618 2.2316 -- 154 1630 0.19 0.2898 -- 97.0
X Ray Diffraction 2.2316 2.3113 -- 133 1698 0.1923 0.2766 -- 100.0
X Ray Diffraction 2.3113 2.4039 -- 128 1699 0.184 0.3049 -- 100.0
X Ray Diffraction 2.4039 2.5133 -- 159 1677 0.1871 0.2385 -- 100.0
X Ray Diffraction 2.5133 2.6457 -- 143 1710 0.1912 0.243 -- 100.0
X Ray Diffraction 2.6457 2.8114 -- 141 1722 0.1934 0.2921 -- 100.0
X Ray Diffraction 2.8114 3.0284 -- 153 1700 0.1818 0.2454 -- 100.0
X Ray Diffraction 3.0284 3.3329 -- 159 1712 0.179 0.2401 -- 100.0
X Ray Diffraction 3.3329 3.8148 -- 145 1743 0.1696 0.203 -- 100.0
X Ray Diffraction 3.8148 4.8044 -- 145 1761 0.1406 0.1722 -- 100.0
X Ray Diffraction 4.8044 35.7852 -- 159 1857 0.1841 0.1958 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 5.8629
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 6.7078
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -12.5707
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.004
f_chiral_restr 0.064
f_dihedral_angle_d 15.729
f_angle_d 1.095
f_bond_d 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2729
Nucleic Acid Atoms 0
Heterogen Atoms 56
Solvent Atoms 237

Software

Computing
Computing Package Purpose
CBASS Data Collection
MOSFLM Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
PHENIX Structure Solution
PHENIX (phenix.refine: 1.7.3_928) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.7.3_928) refinement
PHENIX model building
CBASS data collection