X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 7.5
Temperature 295.0
Details 0.1 M calcium acetate, 0.1M Tris, 25-40% PEG 4000

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 40.17 α = 90
b = 81.1 β = 90
c = 97.58 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 RIGAKU SATURN 944+ -- 2010-11-12
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RU300 0.9793 -- --

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
2.1 37.45 94.7 0.061 -- 28.229 5.9 -- 18372 -- -- --
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)
2.1 2.18 64.6 0.18 -- -- 2.5 --

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 2.096 37.447 -- 0.0 -- 17949 1790 92.58 -- 0.1731 0.1669 0.229 --
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 2.0964 2.1531 -- 83 761 0.2104 0.3069 -- 57.0
X Ray Diffraction 2.1531 2.2164 -- 109 953 0.2104 0.2931 -- 73.0
X Ray Diffraction 2.2164 2.288 -- 129 1158 0.1927 0.2877 -- 89.0
X Ray Diffraction 2.288 2.3697 -- 137 1242 0.1768 0.2549 -- 93.0
X Ray Diffraction 2.3697 2.4646 -- 137 1294 0.1895 0.2632 -- 98.0
X Ray Diffraction 2.4646 2.5767 -- 145 1297 0.1874 0.2675 -- 98.0
X Ray Diffraction 2.5767 2.7126 -- 146 1303 0.1815 0.241 -- 98.0
X Ray Diffraction 2.7126 2.8824 -- 143 1318 0.1857 0.2452 -- 98.0
X Ray Diffraction 2.8824 3.1049 -- 148 1325 0.1987 0.235 -- 99.0
X Ray Diffraction 3.1049 3.4172 -- 148 1328 0.1683 0.2419 -- 99.0
X Ray Diffraction 3.4172 3.9112 -- 151 1349 0.149 0.2226 -- 100.0
X Ray Diffraction 3.9112 4.9259 -- 151 1372 0.1298 0.1913 -- 100.0
X Ray Diffraction 4.9259 37.4526 -- 163 1459 0.1563 0.1884 -- 100.0
RMS Deviations
Key Refinement Restraint Deviation
f_bond_d 0.007
f_plane_restr 0.004
f_dihedral_angle_d 13.76
f_angle_d 0.906
f_chiral_restr 0.049
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2362
Nucleic Acid Atoms 0
Heterogen Atoms 82
Solvent Atoms 301

Software

Software
Software Name Purpose
PHENIX refinement version: 1.10pre_2104
SCALEPACK data scaling
XDS data reduction
PHENIX phasing
PDB_EXTRACT data extraction version: 3.20