X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Microbatch Crystallization Under Oil
pH 6.5
Temperature 277.0
Details 20% PEG MME 5000, 0.1M BIS-TRIS, pH 6.5, Microbatch crystallization under oil, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 44.64 α = 90
b = 95.49 β = 101.8
c = 104.43 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2012-12-19
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 24-ID-E 0.97923 APS 24-ID-E

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
2.49 50 96.9 0.087 -- -- 3.7 59291 57476 0.0 0.0 35.49
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)
2.49 2.6 97.7 0.474 -- 2.6 3.7 7303

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
SAD 2.488 45.061 -- 0.98 -- 57460 2909 96.98 -- 0.195 0.193 0.222 RANDOM
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 2.488 2.528 -- 129 2544 0.349 0.377 -- 95.0
X Ray Diffraction 2.528 2.572 -- 112 2660 0.345 0.4 -- 99.0
X Ray Diffraction 2.572 2.619 -- 141 2720 0.332 0.364 -- 99.0
X Ray Diffraction 2.619 2.669 -- 150 2590 0.298 0.354 -- 99.0
X Ray Diffraction 2.669 2.724 -- 135 2688 0.284 0.332 -- 99.0
X Ray Diffraction 2.724 2.783 -- 148 2650 0.271 0.253 -- 99.0
X Ray Diffraction 2.783 2.848 -- 142 2615 0.248 0.308 -- 99.0
X Ray Diffraction 2.848 2.919 -- 144 2620 0.237 0.252 -- 98.0
X Ray Diffraction 2.919 2.998 -- 118 2691 0.243 0.312 -- 99.0
X Ray Diffraction 2.998 3.086 -- 147 2614 0.225 0.273 -- 98.0
X Ray Diffraction 3.086 3.185 -- 141 2694 0.201 0.22 -- 99.0
X Ray Diffraction 3.185 3.299 -- 133 2594 0.181 0.203 -- 98.0
X Ray Diffraction 3.299 3.431 -- 155 2637 0.189 0.235 -- 98.0
X Ray Diffraction 3.431 3.587 -- 152 2535 0.191 0.227 -- 97.0
X Ray Diffraction 3.587 3.776 -- 131 2584 0.177 0.23 -- 96.0
X Ray Diffraction 3.776 4.013 -- 141 2566 0.141 0.169 -- 96.0
X Ray Diffraction 4.013 4.323 -- 167 2522 0.125 0.134 -- 96.0
X Ray Diffraction 4.323 4.757 -- 120 2551 0.122 0.167 -- 95.0
X Ray Diffraction 4.757 5.444 -- 141 2555 0.15 0.174 -- 95.0
X Ray Diffraction 5.444 6.855 -- 130 2525 0.188 0.219 -- 94.0
X Ray Diffraction 6.855 45.068 -- 132 2396 0.164 0.153 -- 90.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 36.404
Anisotropic B[1][1] 1.298
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -3.636
Anisotropic B[2][2] -5.121
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 3.824
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 15.982
f_plane_restr 0.006
f_chiral_restr 0.09
f_angle_d 1.251
f_bond_d 0.006
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6272
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 146

Software

Computing
Computing Package Purpose
ADSC Quantum Data Collection
XDS Data Reduction (intensity integration)
XScale Data Reduction (data scaling)
phenix.autosol Structure Solution
PHENIX (phenix.refine: 1.7.2_869) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.100 data extraction
phenix refinement