X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8
Temperature 297.0
Details 35% PEG4000, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 297K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 61.87 α = 90
b = 57.56 β = 98.2
c = 79.3 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 315r mirrors 2012-10-10
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 0.97923 APS 19-ID

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
1.85 30 99.9 0.084 -- -- 3.7 47314 47253 -- -3.0 22.9
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)
1.85 1.88 100.0 0.724 -- 1.98 3.7 2354

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 1.85 30.012 -- 0.0 47227 47227 1212 99.78 0.1509 0.1509 0.1496 0.1982 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 1.85 1.9241 -- 133 5091 0.1918 0.218 -- 99.0
X Ray Diffraction 1.9241 2.0116 -- 133 5027 0.1839 0.2417 -- 100.0
X Ray Diffraction 2.0116 2.1177 -- 124 5133 0.1698 0.2375 -- 100.0
X Ray Diffraction 2.1177 2.2503 -- 135 5079 0.1623 0.2503 -- 100.0
X Ray Diffraction 2.2503 2.424 -- 144 5102 0.1546 0.1987 -- 100.0
X Ray Diffraction 2.424 2.6678 -- 133 5113 0.1532 0.2178 -- 100.0
X Ray Diffraction 2.6678 3.0535 -- 140 5125 0.1554 0.2251 -- 100.0
X Ray Diffraction 3.0535 3.8458 -- 143 5143 0.1394 0.1732 -- 100.0
X Ray Diffraction 3.8458 30.0157 -- 127 5202 0.1322 0.1625 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model isotropic
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.007
f_chiral_restr 0.087
f_dihedral_angle_d 13.103
f_angle_d 1.395
f_bond_d 0.014
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4826
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 280

Software

Computing
Computing Package Purpose
SBCcollect Data Collection
HKL-3000 Data Reduction (intensity integration)
HKL-3000 Data Reduction (data scaling)
Phenix, Shelxd, Phaser Structure Solution
PHENIX (phenix.refine: 1.8_1069) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.8_1069) refinement
Phaser model building
Shelxd model building
Phenix model building
SBCcollect data collection