X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.2
Temperature 294.0
Details 31.5% MPD, 90 mM Na/K phosphate, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 294K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 46.78 α = 90
b = 96.57 β = 90
c = 167.89 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 RIGAKU SATURN 92 VariMax HF 2009-05-08
Diffraction Radiation
Monochromator Protocol
VariMaxHF mirrors SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418 -- --

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
2.8 50 98.8 -- 0.069 -- 6.4 -- 19292 0.0 -3.0 --
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)
2.8 2.9 98.5 -- 0.518 2.5 4.0 1883

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
-- 2.8 33.598 -- 0.03 19292 16987 822 87.22 -- 0.2287 0.2259 0.2789 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 2.8 2.9756 -- 111 2198 0.2589 0.3106 -- 73.0
X Ray Diffraction 2.9756 3.2051 -- 131 2380 0.2566 0.324 -- 79.0
X Ray Diffraction 3.2051 3.5274 -- 132 2719 0.2235 0.3253 -- 89.0
X Ray Diffraction 3.5274 4.0371 -- 124 2921 0.2089 0.2605 -- 94.0
X Ray Diffraction 4.0371 5.0834 -- 158 2922 0.1863 0.2366 -- 94.0
X Ray Diffraction 5.0834 33.6003 -- 166 3025 0.24 0.2755 -- 93.0
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.001
f_chiral_restr 0.022
f_dihedral_angle_d 8.784
f_angle_d 0.307
f_bond_d 0.001
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4624
Nucleic Acid Atoms 0
Heterogen Atoms 250
Solvent Atoms 45

Software

Computing
Computing Package Purpose
StructureStudio Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
PHENIX Structure Solution
PHENIX (phenix.refine: 1.5_2) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.5_2) refinement
PHENIX model building
StructureStudio data collection