X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 9
Temperature 291.0
Details A 1.5 UL SOLUTION CONTAINING 26 MG/ML OF PROTEIN, 20 MM MGCL2 AND 20 MM ADP IN 50 MM TRIS-HCL PH 7 WAS MIXED WITH 0.2 M AMMONIUM ACETATE, 0.1 M SODIUM ACETATE TRIHYDRATE PH 5.6, 30% W/V PEG-4000 IN A 1:1 RATIO; VAPOR DIFFUSION; SITTING DROP; 291 K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 64.09 α = 90
b = 64.7 β = 90
c = 86.26 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 ADSC QUANTUM 315r -- 2013-06-12
Diffraction Radiation
Monochromator Protocol
DOUBLE CRYSTAL . SI(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 8.2.1 -- ALS 8.2.1

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
1.59 64.7 100.0 0.09 -- -- 6.5 -- 48649 -- 3.1 15.53
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)
1.59 1.64 100.0 0.62 -- 3.1 6.7 --

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 1.594 40.265 -- 1.34 -- 48566 1030 99.94 -- 0.1825 0.1817 0.2158 --
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 1.5937 1.6777 -- 121 6733 0.2226 0.2537 -- 100.0
X Ray Diffraction 1.6777 1.7828 -- 144 6706 0.2115 0.2657 -- 100.0
X Ray Diffraction 1.7828 1.9205 -- 146 6707 0.2001 0.2338 -- 100.0
X Ray Diffraction 1.9205 2.1138 -- 153 6741 0.1883 0.2213 -- 100.0
X Ray Diffraction 2.1138 2.4196 -- 157 6744 0.1812 0.2152 -- 100.0
X Ray Diffraction 2.4196 3.0483 -- 150 6851 0.1914 0.269 -- 100.0
X Ray Diffraction 3.0483 40.2783 -- 159 7054 0.1597 0.1709 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 20.8
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 18.261
f_plane_restr 0.006
f_angle_d 1.328
f_chiral_restr 0.05
f_bond_d 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3236
Nucleic Acid Atoms 0
Heterogen Atoms 132
Solvent Atoms 334

Software

Software
Software Name Purpose
PHENIX refinement version: (PHENIX.REFINE)
MOSFLM data reduction
SCALA data scaling
MOLREP phasing