X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 293.0
Details 0.16 M zinc acetate, 0.08 M sodium cacodylate, pH 6.5, 20% v/v glycerol, 20% w/v PEG8000, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 84.89 α = 90
b = 80.32 β = 93.85
c = 90.43 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 -- 2010-11-11
Diffraction Radiation
Monochromator Protocol
Double crystal cryo-cooled Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 23-ID-B 1.033 APS 23-ID-B

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
2.5 30 99.7 -- 0.118 -- 3.7 42191 42069 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)
2.5 2.6 99.9 -- 0.51 2.3 3.8 4187

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 2.5 29.141 -- 0.0 42191 41693 2086 98.93 0.2099 0.2099 0.2069 0.2652 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 2.5 2.5582 -- 136 2555 0.3372 0.4236 -- 97.0
X Ray Diffraction 2.5582 2.6221 -- 148 2580 0.3275 0.4045 -- 98.0
X Ray Diffraction 2.6221 2.693 -- 125 2625 0.3051 0.3773 -- 98.0
X Ray Diffraction 2.693 2.7722 -- 141 2637 0.2768 0.3168 -- 99.0
X Ray Diffraction 2.7722 2.8616 -- 114 2630 0.2572 0.3428 -- 98.0
X Ray Diffraction 2.8616 2.9637 -- 141 2607 0.2492 0.3223 -- 99.0
X Ray Diffraction 2.9637 3.0823 -- 141 2667 0.2356 0.2936 -- 99.0
X Ray Diffraction 3.0823 3.2224 -- 138 2606 0.2309 0.3151 -- 99.0
X Ray Diffraction 3.2224 3.392 -- 125 2660 0.2164 0.267 -- 99.0
X Ray Diffraction 3.392 3.6042 -- 153 2649 0.1987 0.2521 -- 100.0
X Ray Diffraction 3.6042 3.8819 -- 133 2671 0.1921 0.2728 -- 99.0
X Ray Diffraction 3.8819 4.2715 -- 161 2642 0.1793 0.2491 -- 100.0
X Ray Diffraction 4.2715 4.887 -- 143 2656 0.1441 0.2002 -- 100.0
X Ray Diffraction 4.887 6.1476 -- 148 2678 0.169 0.2155 -- 99.0
X Ray Diffraction 6.1476 29.1426 -- 139 2744 0.1936 0.2229 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 9.5963
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 8.2532
Anisotropic B[2][2] -6.9369
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.6593
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.007
f_dihedral_angle_d 16.602
f_chiral_restr 0.079
f_angle_d 1.226
f_bond_d 0.011
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6622
Nucleic Acid Atoms 0
Heterogen Atoms 24
Solvent Atoms 165

Software

Software
Software Name Purpose
Blu-Ice data collection
PHASER phasing
PHENIX refinement version: (phenix.refine: 1.7.2_869)
XDS data reduction
XDS data scaling