X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 289.0
Details Peptide was included in protein buffer to a final molar ratio of 2:1 relative to protein. Reservoir solution contained 1.2 M sodium citrate, pH 7.0. Equal amounts (1.5 microliters) of protein (8 mg/mL) and reservoir solution were mixed and equillibrated against 500 microliters of crystallization buffer.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 89.59 α = 90
b = 89.59 β = 90
c = 89.59 γ = 90
Symmetry
Space Group P 41 3 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV++ -- 2012-09-20
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.54178 -- --

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
1.62 40.07 92.53 0.035 -- -- 13.3 -- 15110 -- -- --
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)
-- -- -- 0.338 -- 0.936 1.6 --

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 1.616 40.067 -- 1.46 -- 15110 1513 92.53 -- 0.178 0.1751 0.2033 random selection
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 1.6159 1.6681 -- 45 409 0.311 0.3207 -- 31.0
X Ray Diffraction 1.6681 1.7277 -- 124 1116 0.2394 0.2396 -- 86.0
X Ray Diffraction 1.7277 1.7969 -- 141 1266 0.1915 0.24 -- 99.0
X Ray Diffraction 1.7969 1.8786 -- 146 1315 0.1731 0.2025 -- 100.0
X Ray Diffraction 1.8786 1.9777 -- 146 1318 0.1992 0.2213 -- 100.0
X Ray Diffraction 1.9777 2.1016 -- 147 1311 0.1843 0.2149 -- 100.0
X Ray Diffraction 2.1016 2.2638 -- 147 1326 0.1699 0.2192 -- 100.0
X Ray Diffraction 2.2638 2.4916 -- 149 1342 0.1637 0.1769 -- 100.0
X Ray Diffraction 2.4916 2.8521 -- 149 1337 0.1623 0.2025 -- 100.0
X Ray Diffraction 2.8521 3.593 -- 153 1378 0.1611 0.223 -- 100.0
X Ray Diffraction 3.593 40.0791 -- 166 1479 0.1744 0.1743 -- 100.0
RMS Deviations
Key Refinement Restraint Deviation
f_angle_d 0.945
f_bond_d 0.006
f_chiral_restr 0.048
f_dihedral_angle_d 23.284
f_plane_restr 0.004
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 922
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 148

Software

Software
Software Name Purpose
PHENIX refinement version: 1.10pre_2104
HKL-2000 data reduction
HKL-2000 data scaling
PHENIX phasing
Coot model building