X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 298.0
Details 0-4% PEG 3350, 0.2M ammonium acetate, 0.1M Hepes pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 41.87 α = 79.03
b = 63.05 β = 87.82
c = 73.96 γ = 89.91
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 77
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 6M -- 2013-03-03
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL11-1 1.007 SSRL BL11-1

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
2.58 72.7 95.8 0.195 -- -- 3.2 22899 21938 2.0 2.0 --
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)
2.582 2.74 94.2 0.475 -- 2.1 3.1 3164

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 2.582 61.894 -- 1.97 23296 21929 1107 94.13 -- 0.2109 0.2079 0.2655 imported from structure of wildtype src used as molecular replacement search model
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 2.582 2.7 -- 122 2236 0.2424 0.2823 -- 81.0
X Ray Diffraction 2.7 2.8423 -- 147 2653 0.2282 0.328 -- 96.0
X Ray Diffraction 2.8423 3.0204 -- 117 2670 0.2252 0.2719 -- 96.0
X Ray Diffraction 3.0204 3.2536 -- 150 2633 0.2193 0.2959 -- 96.0
X Ray Diffraction 3.2536 3.581 -- 138 2646 0.2066 0.2675 -- 96.0
X Ray Diffraction 3.581 4.0991 -- 129 2670 0.1944 0.2707 -- 96.0
X Ray Diffraction 4.0991 5.164 -- 152 2679 0.1753 0.2236 -- 97.0
X Ray Diffraction 5.164 61.894 -- 152 2635 0.2264 0.2596 -- 96.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] -2.4068
Anisotropic B[1][2] -0.9842
Anisotropic B[1][3] -0.2223
Anisotropic B[2][2] -7.8552
Anisotropic B[2][3] 5.0364
Anisotropic B[3][3] 10.2621
RMS Deviations
Key Refinement Restraint Deviation
f_chiral_restr 0.074
f_dihedral_angle_d 19.446
f_plane_restr 0.008
f_bond_d 0.008
f_angle_d 1.131
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4272
Nucleic Acid Atoms 0
Heterogen Atoms 72
Solvent Atoms 66

Software

Software
Software Name Purpose
Blu-Ice data collection
PHASER phasing
PHENIX refinement version: (phenix.refine: 1.7_650)
MOSFLM data reduction
SCALA data scaling