X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.6
Temperature 291.15
Details PEG 4000, sodium citrate tribasic dihydrate, pH5.6, glycerol

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 63.21 α = 90
b = 63.21 β = 90
c = 196.14 γ = 90
Symmetry
Space Group P 43 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RAYONIX MX300-HS LN2-Cooled Fixed-Exit Double 2017-03-04
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSRRC BEAMLINE TPS 05A 1.0 NSRRC TPS 05A

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
2.11 30 98.3 0.066 -- -- 7.2 -- 23502 -- -- 45.25
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)
2.11 2.19 92.0 0.621 -- -- 4.9 --

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 2.109 29.482 -- 1.34 -- 23419 1996 98.28 -- 0.1866 0.183 0.2239 --
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 2.1094 2.1622 -- 125 1339 -- 0.3688 0.0 90.0
X Ray Diffraction 2.1622 2.2206 -- 138 1474 -- 0.2657 0.0 97.0
X Ray Diffraction 2.2206 2.2859 -- 140 1493 -- 0.2927 0.0 98.0
X Ray Diffraction 2.2859 2.3597 -- 139 1502 -- 0.2977 0.0 98.0
X Ray Diffraction 2.3597 2.444 -- 140 1508 -- 0.2697 0.0 99.0
X Ray Diffraction 2.444 2.5418 -- 143 1533 -- 0.2642 0.0 99.0
X Ray Diffraction 2.5418 2.6574 -- 142 1521 -- 0.28 0.0 99.0
X Ray Diffraction 2.6574 2.7974 -- 142 1524 -- 0.2856 0.0 99.0
X Ray Diffraction 2.7974 2.9725 -- 142 1534 -- 0.2717 0.0 99.0
X Ray Diffraction 2.9725 3.2018 -- 146 1566 -- 0.2623 0.0 100.0
X Ray Diffraction 3.2018 3.5235 -- 145 1564 -- 0.213 0.0 100.0
X Ray Diffraction 3.5235 4.0323 -- 147 1571 0.1724 0.2176 0.0 100.0
X Ray Diffraction 4.0323 5.076 -- 148 1595 0.1394 0.1896 0.0 99.0
X Ray Diffraction 5.076 29.482 -- 159 1699 0.1639 0.1829 0.0 98.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 64.5664
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_bond_d 0.007
f_chiral_restr 0.052
f_dihedral_angle_d 10.22
f_angle_d 0.83
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2423
Nucleic Acid Atoms 0
Heterogen Atoms 27
Solvent Atoms 47

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
PHASER phasing
PHENIX refinement version: dev_2621
PDB_EXTRACT data extraction version: 3.25