X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6
Temperature 293.15
Details 1.0M MgSO4, 10% glycerol, and 100 mM MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 53.47 α = 90
b = 112.11 β = 90
c = 132.85 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 MARMOSAIC 225 mm CCD -- 2008-07-01
Diffraction Radiation
Monochromator Protocol
Si(III) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 22-BM 1.0 APS 22-BM

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
2.73 49.63 94.0 -- 0.089 -- 6.8 20584 21895 0.0 0.0 --
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)
2.75 2.85 96.1 0.443 -- -- 5.2 --

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 3.0 49.604 -- 1.34 20584 16557 857 99.56 -- 0.2058 0.2029 0.2595 --
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 3.0 3.1881 -- 149 2558 0.2743 0.3556 -- 100.0
X Ray Diffraction 3.1881 3.4342 -- 147 2567 0.2365 0.2769 -- 100.0
X Ray Diffraction 3.4342 3.7797 -- 145 2610 0.1963 0.2493 -- 100.0
X Ray Diffraction 3.7797 4.3263 -- 129 2598 0.1761 0.2411 -- 100.0
X Ray Diffraction 4.3263 5.4496 -- 155 2633 0.1758 0.2565 -- 100.0
X Ray Diffraction 5.4496 49.6112 -- 132 2734 0.2164 0.2433 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 5.412
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.5976
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -7.0096
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.006
f_chiral_restr 0.084
f_dihedral_angle_d 18.081
f_angle_d 1.281
f_bond_d 0.009
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4027
Nucleic Acid Atoms 0
Heterogen Atoms 135
Solvent Atoms 13

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
PHASES Structure Solution
PHENIX (phenix.refine: 1.7.1_743) Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.5.0110 refinement
PHASES model building
HKL-2000 data collection