X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.8
Temperature 291.0
Details Protein solution: 10 - 16 mg/mL, 50 mM HEPES, pH 7.2, 50 mM NaCl, 10mM MgCl2 5% Glycerol, 1mM DTE, 10 M ZnCl2 Reservoir solution:200mM calcium acetate, 100mM sodium cacodylate pH 6.5, 18% PEG 8000. Drop: 1uL protein, 1uL reservoir, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 90.44 α = 90
b = 90.44 β = 90
c = 92.7 γ = 120
Symmetry
Space Group P 3 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD -- --
Diffraction Radiation
Monochromator Protocol
crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 23-ID-D 1.0 APS 23-ID-D

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
2.45 32.4 -- 0.15 -- -- 8.9 16218 16218 3.0 3.0 --

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
-- 2.45 32.368 -- 1.34 -- 16133 1628 97.08 -- 0.1858 0.1809 0.2294 --
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 2.4459 2.5178 -- 112 930 0.2724 0.2884 -- 77.0
X Ray Diffraction 2.5178 2.5991 -- 125 1138 0.2444 0.2859 -- 92.0
X Ray Diffraction 2.5991 2.6919 -- 135 1194 0.2416 0.315 -- 98.0
X Ray Diffraction 2.6919 2.7996 -- 136 1225 0.2275 0.2771 -- 99.0
X Ray Diffraction 2.7996 2.927 -- 137 1212 0.2074 0.2585 -- 99.0
X Ray Diffraction 2.927 3.0812 -- 139 1238 0.1923 0.278 -- 100.0
X Ray Diffraction 3.0812 3.274 -- 137 1223 0.1875 0.261 -- 100.0
X Ray Diffraction 3.274 3.5266 -- 136 1234 0.172 0.2133 -- 99.0
X Ray Diffraction 3.5266 3.8809 -- 139 1244 0.1563 0.2208 -- 100.0
X Ray Diffraction 3.8809 4.4413 -- 140 1255 0.1452 0.1776 -- 100.0
X Ray Diffraction 4.4413 5.5908 -- 138 1279 0.1568 0.2138 -- 100.0
X Ray Diffraction 5.5908 32.3708 -- 154 1333 0.1929 0.2179 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 7.1703
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 7.1703
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -14.3406
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.003
f_chiral_restr 0.04
f_dihedral_angle_d 14.171
f_angle_d 0.68
f_bond_d 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1875
Nucleic Acid Atoms 0
Heterogen Atoms 47
Solvent Atoms 82

Software

Computing
Computing Package Purpose
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
PHENIX Structure Solution
PHENIX (phenix.refine: 1.8.2_1309) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.7.3_928) refinement
PHENIX model building