X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 8.5
Temperature 277.0
Details 200 mM potassium sodium tartrate, 20% w/v PEG3350, pH 8.5, VAPOR DIFFUSION, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 40.43 α = 90
b = 116.21 β = 90
c = 117.14 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 300 mm CCD -- 2012-12-10
Diffraction Radiation
Monochromator Protocol
Rosenbaum-Rock double-crystal Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 22-ID 1.000 APS 22-ID

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
1.94 50 99.9 0.078 -- -- 4.0 41560 41518 1.0 1.0 --
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)
1.944 2.02 99.9 0.588 -- -- 3.9 4096

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 1.944 32.409 -- 1.36 41560 41440 2082 99.69 -- 0.1729 0.1712 0.2047 RANDOM
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 1.944 1.9894 -- 120 2505 0.2448 0.317 -- 97.0
X Ray Diffraction 1.9894 2.0391 -- 140 2603 0.2279 0.2697 -- 100.0
X Ray Diffraction 2.0391 2.0943 -- 130 2575 0.2172 0.283 -- 100.0
X Ray Diffraction 2.0943 2.1559 -- 150 2595 0.1896 0.2493 -- 100.0
X Ray Diffraction 2.1559 2.2254 -- 131 2597 0.1895 0.2317 -- 100.0
X Ray Diffraction 2.2254 2.305 -- 149 2563 0.181 0.2277 -- 100.0
X Ray Diffraction 2.305 2.3972 -- 136 2617 0.1861 0.2207 -- 100.0
X Ray Diffraction 2.3972 2.5063 -- 135 2618 0.1878 0.205 -- 100.0
X Ray Diffraction 2.5063 2.6384 -- 130 2612 0.186 0.2386 -- 100.0
X Ray Diffraction 2.6384 2.8036 -- 140 2620 0.185 0.2474 -- 100.0
X Ray Diffraction 2.8036 3.0199 -- 145 2616 0.1843 0.2261 -- 100.0
X Ray Diffraction 3.0199 3.3235 -- 135 2664 0.1552 0.1954 -- 100.0
X Ray Diffraction 3.3235 3.8038 -- 155 2629 0.1462 0.1636 -- 100.0
X Ray Diffraction 3.8038 4.7899 -- 125 2722 0.1361 0.1602 -- 100.0
X Ray Diffraction 4.7899 32.4135 -- 161 2822 0.1682 0.1726 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 24.6341
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 20.704
f_plane_restr 0.004
f_chiral_restr 0.066
f_angle_d 1.154
f_bond_d 0.009
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2954
Nucleic Acid Atoms 818
Heterogen Atoms 58
Solvent Atoms 556

Software

Computing
Computing Package Purpose
SER-gui Data Collection
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
phenix.refine Structure Solution
PHENIX (phenix.refine: 1.8.1_1168) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
SCALEPACK data reduction