X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5.6
Temperature 292.0
Details 0.1M Sodium Citrate, 0.5M Ammonium Acetate, 14% PEG 4000, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 292K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 103.38 α = 90
b = 127.4 β = 100.5
c = 148.99 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 315r -- 2008-10-04
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID23-1 0.9537,1.2546 ESRF ID23-1

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
3.4 58.42 99.7 0.089 0.105 -- 3.5 52274 52431 1.3 1.0 --
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)
3.4 3.58 100.0 0.578 0.68 2.3 3.6 --

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
SAD 3.4 29.915 -- 0.91 102713 101419 5051 98.74 -- 0.2673 0.265 0.3127 --
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 3.4 3.4386 -- 200 3329 0.3821 0.4549 -- 99.0
X Ray Diffraction 3.4386 3.479 -- 202 3073 0.3646 0.3992 -- 99.0
X Ray Diffraction 3.479 3.5213 -- 153 3229 0.3623 0.4137 -- 99.0
X Ray Diffraction 3.5213 3.5658 -- 169 3322 0.3528 0.4195 -- 99.0
X Ray Diffraction 3.5658 3.6127 -- 183 3108 0.3533 0.4138 -- 99.0
X Ray Diffraction 3.6127 3.6621 -- 174 3265 0.3406 0.3898 -- 99.0
X Ray Diffraction 3.6621 3.7143 -- 153 3243 0.3003 0.3454 -- 99.0
X Ray Diffraction 3.7143 3.7697 -- 172 3194 0.2815 0.3723 -- 99.0
X Ray Diffraction 3.7697 3.8284 -- 187 3293 0.2768 0.3254 -- 99.0
X Ray Diffraction 3.8284 3.8911 -- 146 3182 0.2872 0.3275 -- 99.0
X Ray Diffraction 3.8911 3.958 -- 174 3240 0.2825 0.3821 -- 99.0
X Ray Diffraction 3.958 4.0298 -- 128 3278 0.2816 0.3002 -- 100.0
X Ray Diffraction 4.0298 4.1072 -- 161 3329 0.2717 0.4058 -- 100.0
X Ray Diffraction 4.1072 4.1908 -- 158 3195 0.2519 0.2623 -- 100.0
X Ray Diffraction 4.1908 4.2816 -- 211 3185 0.2524 0.3356 -- 100.0
X Ray Diffraction 4.2816 4.3809 -- 198 3194 0.2341 0.2717 -- 100.0
X Ray Diffraction 4.3809 4.4902 -- 146 3307 0.2274 0.2882 -- 100.0
X Ray Diffraction 4.4902 4.6111 -- 172 3210 0.2253 0.2861 -- 100.0
X Ray Diffraction 4.6111 4.7463 -- 174 3274 0.2354 0.2994 -- 100.0
X Ray Diffraction 4.7463 4.8989 -- 170 3268 0.2336 0.2931 -- 100.0
X Ray Diffraction 4.8989 5.0731 -- 140 3244 0.2247 0.306 -- 100.0
X Ray Diffraction 5.0731 5.2752 -- 171 3231 0.2376 0.304 -- 100.0
X Ray Diffraction 5.2752 5.5139 -- 175 3270 0.2598 0.3338 -- 100.0
X Ray Diffraction 5.5139 5.8026 -- 170 3221 0.2665 0.3492 -- 99.0
X Ray Diffraction 5.8026 6.1632 -- 172 3207 0.2586 0.3334 -- 100.0
X Ray Diffraction 6.1632 6.6343 -- 149 3236 0.2456 0.2564 -- 99.0
X Ray Diffraction 6.6343 7.2931 -- 168 3202 0.2187 0.2595 -- 99.0
X Ray Diffraction 7.2931 8.3285 -- 171 3041 0.2043 0.2444 -- 93.0
X Ray Diffraction 8.3285 10.4188 -- 189 3129 0.1748 0.1989 -- 97.0
X Ray Diffraction 10.4188 29.9161 -- 115 2869 0.2806 0.2903 -- 87.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model isotropic
Anisotropic B[1][1] 1.4017
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 7.917
Anisotropic B[2][2] 6.68
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -8.0817
RMS Deviations
Key Refinement Restraint Deviation
f_chiral_restr 0.073
f_bond_d 0.01
f_plane_restr 0.004
f_angle_d 1.298
f_dihedral_angle_d 17.474
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 23034
Nucleic Acid Atoms 0
Heterogen Atoms 162
Solvent Atoms 0

Software

Software
Software Name Purpose
DNA data collection
PHASES phasing
PHENIX refinement version: (phenix.refine: dev_249)
MOSFLM data reduction
SCALA data scaling