X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.9
Temperature 298.0
Details 10% PEG-3350, 100 mM Ca(OAc)2, 100 mM MES/Tris, 2.5% Glycerol, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 52.82 α = 90
b = 99.65 β = 90.16
c = 101.62 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2012-02-06
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X29A 1.075 NSLS X29A

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
1.9 30 96.5 0.039 -- -- 3.5 83084 80176 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)
1.9 1.93 81.1 0.166 -- 3.8 2.5 3345

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 1.898 28.014 -- 1.54 -- 80155 1927 96.52 -- 0.1873 0.1865 0.2189 --
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 1.898 1.9458 -- 124 4854 0.219 0.2484 -- 83.0
X Ray Diffraction 1.9458 1.9983 -- 129 5374 0.2049 0.2602 -- 94.0
X Ray Diffraction 1.9983 2.0571 -- 138 5456 0.1945 0.2034 -- 95.0
X Ray Diffraction 2.0571 2.1235 -- 140 5562 0.1937 0.2428 -- 96.0
X Ray Diffraction 2.1235 2.1994 -- 131 5606 0.1948 0.2405 -- 97.0
X Ray Diffraction 2.1994 2.2874 -- 139 5606 0.2003 0.2015 -- 97.0
X Ray Diffraction 2.2874 2.3914 -- 131 5637 0.2009 0.2822 -- 98.0
X Ray Diffraction 2.3914 2.5175 -- 142 5670 0.2004 0.243 -- 98.0
X Ray Diffraction 2.5175 2.6751 -- 139 5692 0.2009 0.29 -- 99.0
X Ray Diffraction 2.6751 2.8814 -- 135 5712 0.2084 0.2744 -- 99.0
X Ray Diffraction 2.8814 3.171 -- 139 5770 0.1987 0.2005 -- 99.0
X Ray Diffraction 3.171 3.629 -- 143 5752 0.1813 0.2133 -- 99.0
X Ray Diffraction 3.629 4.569 -- 148 5788 0.1586 0.184 -- 99.0
X Ray Diffraction 4.569 28.0171 -- 149 5749 0.1754 0.1943 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] -4.1495
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.2172
Anisotropic B[2][2] 6.1347
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.9852
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.006
f_chiral_restr 0.079
f_dihedral_angle_d 18.228
f_angle_d 1.493
f_bond_d 0.011
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5476
Nucleic Acid Atoms 1142
Heterogen Atoms 60
Solvent Atoms 708

Software

Computing
Computing Package Purpose
CBASS Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
PHASER in 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
PHASER version: in PHENIX model building
CBASS data collection