X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.6
Temperature 298.0
Details 100mM sodium citrate, 100mM MgCl2, 16-18% PEG 3350, 2mM UTP, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 45.31 α = 90
b = 66.78 β = 90
c = 119.55 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 -- 2012-09-26
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X25 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
2.03 46.1 100.0 -- -- -- -- 24709 24709 -999.0 -999.0 --
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)
2.03 2.08 100.0 -- -- -- -- --

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
Direct refinement 2.03 44.538 -- 1.34 24153 24105 1901 99.76 -- 0.1745 0.1701 0.2244 --
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 2.03 2.0809 -- 133 1538 0.1939 0.2728 -- 99.0
X Ray Diffraction 2.0809 2.1372 -- 132 1551 0.2064 0.2653 -- 100.0
X Ray Diffraction 2.1372 2.2 -- 131 1546 0.189 0.2441 -- 100.0
X Ray Diffraction 2.2 2.2711 -- 135 1574 0.1892 0.2728 -- 100.0
X Ray Diffraction 2.2711 2.3522 -- 133 1549 0.189 0.2945 -- 100.0
X Ray Diffraction 2.3522 2.4464 -- 137 1580 0.1821 0.2821 -- 100.0
X Ray Diffraction 2.4464 2.5577 -- 134 1569 0.1871 0.2423 -- 100.0
X Ray Diffraction 2.5577 2.6926 -- 134 1569 0.19 0.2619 -- 100.0
X Ray Diffraction 2.6926 2.8612 -- 134 1574 0.1781 0.2233 -- 100.0
X Ray Diffraction 2.8612 3.0821 -- 136 1590 0.1847 0.2209 -- 100.0
X Ray Diffraction 3.0821 3.3922 -- 137 1596 0.1713 0.2462 -- 100.0
X Ray Diffraction 3.3922 3.8828 -- 138 1613 0.1608 0.218 -- 100.0
X Ray Diffraction 3.8828 4.8909 -- 140 1630 0.1318 0.1529 -- 100.0
X Ray Diffraction 4.8909 44.5489 -- 147 1725 0.1581 0.1966 -- 100.0
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_chiral_restr 0.072
f_dihedral_angle_d 17.189
f_angle_d 1.26
f_bond_d 0.009
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2738
Nucleic Acid Atoms 0
Heterogen Atoms 61
Solvent Atoms 266

Software

Computing
Computing Package Purpose
CBASS Data Collection
MOSFLM Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
PHENIX Structure Solution
PHENIX (phenix.refine: 1.8.1_1168) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.8.1_1168) refinement
PHENIX model building
CBASS data collection