X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Sitting Drop
pH 7.5
Temperature 277.0
Details 30% butanol, 0.2 M sodium chloride, 0.1 M Tris, 0.5% N,N-dimethyldodecylamine-N-oxide, pH 7.5, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 105.15 α = 90
b = 65.81 β = 109
c = 108.5 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 ADSC QUANTUM 4 -- 2010-10-15
Diffraction Radiation
Monochromator Protocol
KOHZU double crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X4A 0.979 NSLS X4A

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
2.69 102.59 92.7 0.113 -- -- 3.2 39473 36583 -3.0 -3.0 45.658
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)
2.689 2.85 92.6 0.625 -- 2.34 -- --

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 2.689 34.196 -- 1.99 36552 36552 1838 92.79 -- 0.2218 0.2201 0.2536 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 2.689 2.7618 -- 136 2587 0.3208 0.366 -- 89.0
X Ray Diffraction 2.7618 2.843 -- 131 2719 0.2819 0.3729 -- 96.0
X Ray Diffraction 2.843 2.9347 -- 133 2703 0.2686 0.3084 -- 95.0
X Ray Diffraction 2.9347 3.0395 -- 163 2715 0.2586 0.2874 -- 95.0
X Ray Diffraction 3.0395 3.1612 -- 142 2728 0.244 0.2908 -- 95.0
X Ray Diffraction 3.1612 3.3049 -- 139 2705 0.2297 0.3012 -- 95.0
X Ray Diffraction 3.3049 3.479 -- 156 2681 0.2355 0.2978 -- 94.0
X Ray Diffraction 3.479 3.6967 -- 131 2685 0.2669 0.3077 -- 93.0
X Ray Diffraction 3.6967 3.9818 -- 142 2656 0.2139 0.2498 -- 93.0
X Ray Diffraction 3.9818 4.3817 -- 127 2686 0.1702 0.193 -- 92.0
X Ray Diffraction 4.3817 5.0141 -- 149 2636 0.1592 0.158 -- 92.0
X Ray Diffraction 5.0141 6.3107 -- 129 2615 0.1962 0.2231 -- 90.0
X Ray Diffraction 6.3107 34.1992 -- 160 2598 0.2041 0.2297 -- 88.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 46.7215
Anisotropic B[1][1] 3.6729
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 7.2874
Anisotropic B[2][2] -6.1284
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 7.6137
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 12.247
f_plane_restr 0.003
f_chiral_restr 0.049
f_angle_d 0.715
f_bond_d 0.003
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5370
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 287

Software

Computing
Computing Package Purpose
ADSC Quantum Data Collection
XDS Data Reduction (intensity integration)
XDS Data Reduction (data scaling)
Phaser Structure Solution
PHENIX (phenix.refine: dev_1000) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
Xscale data reduction