X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8
Temperature 291.0
Details 50mM Imidazole, 350mM NaCl, 17% PEG3350, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 54.98 α = 90
b = 78.51 β = 113.24
c = 55.14 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 MARMOSAIC 300 mm CCD vertical focusing mirrors 2012-10-07
Diffraction Radiation
Monochromator Protocol
Rosenbaum-Rock double-crystal Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 22-ID 1.00 APS 22-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
2 50 93.0 0.058 -- -- 3.5 29102 n/a 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)
2.0 2.03 97.8 0.405 -- -- 3.0 1433

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 2.002 39.674 -- 0.0 -- 48505 2422 84.94 -- 0.2191 0.2159 0.2806 --
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 2.0 2.04 2208 110 -- 0.2891 0.3415 -- 68.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 39.4944
Anisotropic B[1][1] -0.871
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 4.4423
Anisotropic B[2][2] -2.7567
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 3.6276
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 22.631
f_bond_d 0.014
f_plane_restr 0.004
f_angle_d 1.178
f_chiral_restr 0.069
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2598
Nucleic Acid Atoms 632
Heterogen Atoms 38
Solvent Atoms 165

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
PHASER phasing
REFMAC refinement
PDB_EXTRACT data extraction version: 3.11
HKL-2000 data collection
PHENIX refinement version: 1.7_650