X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.2
Temperature 289.0
Details 12% PEG 5000 MME, 0.1 M MES, O.1 M Ammonium sulfate, 5% glycerol, 1.8 mM UDM, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 114.35 α = 90
b = 114.35 β = 90
c = 170.68 γ = 120
Symmetry
Space Group P 64 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD PSI PILATUS 6M -- 2012-07-18
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X25 1.1 NSLS X25

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
4.15 40 99.8 0.075 -- -- 12.6 5449 5438 2.8 1.4 --
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)
4.15 4.22 100.0 -- -- -- 13.5 263

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 4.15 19.988 -- 1.39 5337 5331 245 99.85 -- 0.2617 0.2593 0.3112 --
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 4.15 5.2132 -- 128 2467 0.2749 0.3602 -- 100.0
X Ray Diffraction 5.2132 19.9883 -- 117 2619 0.2544 0.294 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 173.168
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 12.511
f_plane_restr 0.003
f_chiral_restr 0.05
f_angle_d 0.798
f_bond_d 0.004
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3252
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 5

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 1.8_1069) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
Phaser molecular replacement
SCALEPACK data reduction