X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.5
Temperature 298.0
Details 30% w/v PEG 4000 0.2M Magnesium chloride 0.1M TRIS hydrochloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 42.01 α = 90
b = 71.53 β = 90
c = 74.57 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
IMAGE PLATE RIGAKU RAXIS IV++ -- 2011-09-22
Diffraction Radiation
Monochromator Protocol
Varimax Optics SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RUH3R 1.5418 -- --

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
1.73 20 84.9 0.102 -- -- 5.4 24057 20425 -- -- --
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)
1.729 1.8 99.7 0.362 -- -- 5.9 --

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 1.73 19.46 -- -- 24143 20121 1978 83.3 -- 0.201 0.195 0.253 --
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 1.73 1.7725 -- 134 1357 0.3015 0.3631 -- 89.0
X Ray Diffraction 1.7725 1.8204 -- 173 1493 0.2613 0.3116 -- 97.0
X Ray Diffraction 1.8204 1.8739 -- 159 1460 0.218 0.2773 -- 96.0
X Ray Diffraction 1.8739 1.9344 -- 52 499 0.2013 0.2797 -- 32.0
X Ray Diffraction 1.9344 2.0034 -- 155 1425 0.2073 0.2938 -- 94.0
X Ray Diffraction 2.0034 2.0836 -- 173 1503 0.1919 0.2706 -- 98.0
X Ray Diffraction 2.0836 2.1783 -- 161 1514 0.195 0.2804 -- 99.0
X Ray Diffraction 2.1783 2.2929 -- 62 625 0.2068 0.2745 -- 40.0
X Ray Diffraction 2.2929 2.4363 -- 174 1513 0.1938 0.2538 -- 98.0
X Ray Diffraction 2.4363 2.624 -- 168 1531 0.1996 0.2954 -- 98.0
X Ray Diffraction 2.624 2.8873 -- 167 1539 0.2019 0.255 -- 99.0
X Ray Diffraction 2.8873 3.3034 -- 165 1533 0.2103 0.2646 -- 97.0
X Ray Diffraction 3.3034 4.1552 -- 57 527 0.1793 0.2483 -- 33.0
X Ray Diffraction 4.1552 19.4591 -- 178 1624 0.16 0.1816 -- 97.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 26.91
Anisotropic B[1][1] -4.2896
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 4.2856
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.004
RMS Deviations
Key Refinement Restraint Deviation
f_chiral_restr 0.083
f_plane_restr 0.007
f_bond_d 0.012
f_angle_d 1.368
f_dihedral_angle_d 13.813
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2047
Nucleic Acid Atoms 0
Heterogen Atoms 2
Solvent Atoms 89

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
PHENIX refinement version: 1.7.2_869
PDB_EXTRACT data extraction version: 3.10
CrystalClear data collection
PHENIX phasing