X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
Temperature 277.0
Details 0.1 M sodium cacodylate pH 7.0 and 1.0 M sodium acetate trihydrate

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 55.75 α = 90
b = 62.85 β = 90
c = 140.08 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 325 mm CCD -- 2015-02-25
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL14-1 0.9795 SSRL BL14-1

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
1.72 70.04 100.0 -- -- -- 7.2 52778 52702 -- -- --
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)
-- -- -- -- -- -- -- --

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
-- 1.724 41.706 -- 1.34 -- 52694 2598 99.91 -- 0.1982 0.1969 0.224 --
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 1.7244 1.7558 -- 137 2620 0.2597 0.2768 -- 100.0
X Ray Diffraction 1.7558 1.7895 -- 130 2601 0.2503 0.2783 -- 100.0
X Ray Diffraction 1.7895 1.8261 -- 124 2594 0.2396 0.2567 -- 100.0
X Ray Diffraction 1.8261 1.8658 -- 153 2587 0.2345 0.2647 -- 100.0
X Ray Diffraction 1.8658 1.9092 -- 151 2612 0.2397 0.2622 -- 100.0
X Ray Diffraction 1.9092 1.9569 -- 125 2577 0.2398 0.2871 -- 100.0
X Ray Diffraction 1.9569 2.0098 -- 142 2599 0.2126 0.2429 -- 100.0
X Ray Diffraction 2.0098 2.069 -- 138 2607 0.2089 0.253 -- 100.0
X Ray Diffraction 2.069 2.1357 -- 108 2641 0.2073 0.241 -- 100.0
X Ray Diffraction 2.1357 2.2121 -- 133 2624 0.2025 0.2369 -- 100.0
X Ray Diffraction 2.2121 2.3006 -- 140 2599 0.2099 0.2362 -- 100.0
X Ray Diffraction 2.3006 2.4053 -- 156 2623 0.212 0.247 -- 100.0
X Ray Diffraction 2.4053 2.5321 -- 139 2616 0.2135 0.2672 -- 100.0
X Ray Diffraction 2.5321 2.6907 -- 119 2666 0.213 0.2461 -- 100.0
X Ray Diffraction 2.6907 2.8984 -- 151 2635 0.2117 0.2213 -- 100.0
X Ray Diffraction 2.8984 3.19 -- 130 2658 0.1993 0.2255 -- 100.0
X Ray Diffraction 3.19 3.6514 -- 136 2699 0.1816 0.2146 -- 100.0
X Ray Diffraction 3.6514 4.5994 -- 138 2703 0.1622 0.1835 -- 100.0
X Ray Diffraction 4.5994 41.7183 -- 148 2835 0.1752 0.1919 -- 99.0
RMS Deviations
Key Refinement Restraint Deviation
f_bond_d 0.007
f_angle_d 1.071
f_chiral_restr 0.043
f_plane_restr 0.005
f_dihedral_angle_d 17.483
Coordinate Error
Parameter Value
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2388
Nucleic Acid Atoms 427
Heterogen Atoms 30
Solvent Atoms 409

Software

Software
Software Name Purpose
PHENIX refinement version: 1.9_1692
XDS data reduction
Aimless data scaling
PHASER phasing