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 dATP, 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
2.01 45.5 99.7 -- -- -- -- 24436 24363 -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)
2.01 2.07 99.2 -- -- -- -- --

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 2.01 44.538 -- 1.35 24577 24307 1916 98.07 -- 0.159 0.1538 0.2176 --
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 2.01 2.063 -- 106 1277 0.1513 0.2544 -- 80.0
X Ray Diffraction 2.063 2.1188 -- 135 1573 0.1487 0.2006 -- 99.0
X Ray Diffraction 2.1188 2.1812 -- 135 1596 0.1382 0.2172 -- 99.0
X Ray Diffraction 2.1812 2.2516 -- 138 1596 0.139 0.1974 -- 99.0
X Ray Diffraction 2.2516 2.332 -- 136 1568 0.1449 0.2158 -- 99.0
X Ray Diffraction 2.332 2.4254 -- 136 1604 0.164 0.2602 -- 100.0
X Ray Diffraction 2.4254 2.5358 -- 140 1627 0.1625 0.2686 -- 99.0
X Ray Diffraction 2.5358 2.6695 -- 139 1621 0.1679 0.2463 -- 99.0
X Ray Diffraction 2.6695 2.8367 -- 138 1604 0.1545 0.2286 -- 100.0
X Ray Diffraction 2.8367 3.0557 -- 139 1620 0.1613 0.2055 -- 99.0
X Ray Diffraction 3.0557 3.3631 -- 140 1630 0.1561 0.2218 -- 100.0
X Ray Diffraction 3.3631 3.8495 -- 141 1647 0.1434 0.2047 -- 100.0
X Ray Diffraction 3.8495 4.849 -- 143 1668 0.1333 0.1847 -- 100.0
X Ray Diffraction 4.849 44.549 -- 150 1760 0.1814 0.2271 -- 99.0
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.006
f_chiral_restr 0.078
f_dihedral_angle_d 16.235
f_angle_d 1.273
f_bond_d 0.01
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2738
Nucleic Acid Atoms 0
Heterogen Atoms 63
Solvent Atoms 279

Software

Computing
Computing Package Purpose
CBASS Data Collection
MOSFLM Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
PHENIX Structure Solution
PHENIX (phenix.refine: 1.8.2_1309) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.8.1_1168) refinement
PHENIX model building
CBASS data collection