X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 294.0
Details 1.6 - 2.0 M Ammonium Phosphate, 0.1mM HEPES, pH 7.5, 1mM DTT, VAPOR DIFFUSION, SITTING DROP, temperature 294K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 227.37 α = 90
b = 104.14 β = 93.78
c = 81.32 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD PSI PILATUS 6M Si(111) 2010-11-08
Diffraction Radiation
Monochromator Protocol
Double silicon(111) crystal monochromator with cryogenically-cooled first crystal and sagittally-bent second crystal horizontally-focusing at 3.3:1 demagnification MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X25 0.979, 1.1 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
2.8 29.9 98.16 0.51 -- -- 3.9 -- 46664 0.0 0.0 77.3
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)
2.8 2.86 99.8 0.032 -- 29.4 4.1 4750

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
MAD 2.801 29.9 -- 0.0 45768 45768 2287 98.16 0.1865 0.1865 0.1845 0.2226 5%
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 2.8012 2.8621 -- 115 2205 0.3281 0.4184 -- 81.0
X Ray Diffraction 2.8621 2.9286 -- 119 2577 0.303 0.3682 -- 93.0
X Ray Diffraction 2.9286 3.0018 -- 146 2702 0.2686 0.3111 -- 98.0
X Ray Diffraction 3.0018 3.0829 -- 152 2730 0.2519 0.3027 -- 99.0
X Ray Diffraction 3.0829 3.1735 -- 140 2742 0.2254 0.265 -- 100.0
X Ray Diffraction 3.1735 3.2758 -- 156 2761 0.2169 0.2421 -- 100.0
X Ray Diffraction 3.2758 3.3927 -- 142 2780 0.203 0.2776 -- 100.0
X Ray Diffraction 3.3927 3.5283 -- 145 2732 0.1823 0.2531 -- 100.0
X Ray Diffraction 3.5283 3.6887 -- 135 2774 0.1733 0.219 -- 100.0
X Ray Diffraction 3.6887 3.8827 -- 156 2760 0.1669 0.1873 -- 100.0
X Ray Diffraction 3.8827 4.1254 -- 154 2769 0.1505 0.2034 -- 100.0
X Ray Diffraction 4.1254 4.443 -- 157 2729 0.1403 0.1865 -- 100.0
X Ray Diffraction 4.443 4.8884 -- 125 2798 0.1305 0.1577 -- 100.0
X Ray Diffraction 4.8884 5.5918 -- 155 2773 0.1544 0.1935 -- 100.0
X Ray Diffraction 5.5918 7.03 -- 134 2814 0.2071 0.2515 -- 100.0
X Ray Diffraction 7.03 29.9644 -- 156 2835 0.2004 0.202 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] -4.5688
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -3.3581
Anisotropic B[2][2] 11.5406
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -6.9718
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_chiral_restr 0.08
f_dihedral_angle_d 16.743
f_angle_d 1.181
f_bond_d 0.009
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7469
Nucleic Acid Atoms 0
Heterogen Atoms 60
Solvent Atoms 91

Software

Computing
Computing Package Purpose
CBASS Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
SOLVE Structure Solution
PHENIX (phenix.refine: 1.7.1_743) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.7.1_743) refinement
SOLVE model building
CBASS data collection