X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 295.7
Details 10% PEG6000, 0.1 M HEPES, pH 7.5, vapor diffusion, sitting drop, temperature 295.7K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 126.84 α = 90
b = 133.14 β = 90
c = 812.99 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
PIXEL DECTRIS PILATUS 6M Shutterless data collection; Fine phi slicing experiments 2012-01-11
Diffraction Radiation
Monochromator Protocol
Liquid nitrogen-cooled double crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL12-2 0.97950 SSRL BL12-2

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
3.15 50 98.7 0.133 -- -- 6.6 -- 234983 -- -- --
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)
3.15 3.26 95.6 0.819 -- -- 5.5 --

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 3.2 48.13 -- 0.0 -- 205778 10333 90.25 -- 0.2517 0.249 0.3019 --
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 3.2 3.2364 -- 57 1077 0.3615 0.3956 -- 15.0
X Ray Diffraction 3.2364 3.2744 -- 98 1915 0.3521 0.4125 -- 27.0
X Ray Diffraction 3.2744 3.3144 -- 138 2975 0.333 0.3835 -- 42.0
X Ray Diffraction 3.3144 3.3563 -- 232 4554 0.3313 0.3823 -- 64.0
X Ray Diffraction 3.3563 3.4004 -- 303 6048 0.3262 0.4054 -- 84.0
X Ray Diffraction 3.4004 3.447 -- 368 6962 0.3248 0.3747 -- 98.0
X Ray Diffraction 3.447 3.4962 -- 380 7122 0.3158 0.3404 -- 100.0
X Ray Diffraction 3.4962 3.5484 -- 383 7116 0.3117 0.3513 -- 100.0
X Ray Diffraction 3.5484 3.6038 -- 358 7203 0.2986 0.37 -- 100.0
X Ray Diffraction 3.6038 3.6629 -- 390 7032 0.2925 0.3695 -- 100.0
X Ray Diffraction 3.6629 3.7261 -- 333 6831 0.2796 0.3411 -- 95.0
X Ray Diffraction 3.7261 3.7938 -- 365 7024 0.274 0.3449 -- 99.0
X Ray Diffraction 3.7938 3.8667 -- 392 7143 0.2685 0.3256 -- 100.0
X Ray Diffraction 3.8667 3.9456 -- 375 7161 0.2712 0.3244 -- 100.0
X Ray Diffraction 3.9456 4.0314 -- 402 7155 0.2344 0.3204 -- 100.0
X Ray Diffraction 4.0314 4.1251 -- 347 7165 0.2362 0.2843 -- 100.0
X Ray Diffraction 4.1251 4.2282 -- 389 7204 0.2268 0.2677 -- 100.0
X Ray Diffraction 4.2282 4.3424 -- 420 7130 0.2193 0.2638 -- 100.0
X Ray Diffraction 4.3424 4.4701 -- 386 7177 0.2067 0.2511 -- 100.0
X Ray Diffraction 4.4701 4.6143 -- 372 6884 0.2095 0.261 -- 96.0
X Ray Diffraction 4.6143 4.7791 -- 379 7147 0.2053 0.2871 -- 99.0
X Ray Diffraction 4.7791 4.9702 -- 430 7194 0.201 0.25 -- 100.0
X Ray Diffraction 4.9702 5.1962 -- 366 7202 0.2047 0.2621 -- 100.0
X Ray Diffraction 5.1962 5.4698 -- 389 7235 0.2211 0.2488 -- 100.0
X Ray Diffraction 5.4698 5.812 -- 379 7293 0.2386 0.297 -- 100.0
X Ray Diffraction 5.812 6.2598 -- 349 7042 0.2442 0.3292 -- 97.0
X Ray Diffraction 6.2598 6.8881 -- 395 7295 0.2323 0.2896 -- 100.0
X Ray Diffraction 6.8881 7.8811 -- 381 7397 0.2157 0.2741 -- 100.0
X Ray Diffraction 7.8811 9.9151 -- 381 7252 0.2026 0.2472 -- 98.0
X Ray Diffraction 9.9151 48.1353 -- 396 7510 0.2884 0.3232 -- 97.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] -4.7199
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -3.6156
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -7.4957
RMS Deviations
Key Refinement Restraint Deviation
f_angle_d 1.366
f_plane_restr 0.007
f_dihedral_angle_d 20.838
f_chiral_restr 0.088
f_bond_d 0.01
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 58356
Nucleic Acid Atoms 0
Heterogen Atoms 386
Solvent Atoms 0

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
PHENIX refinement version: 1.7.2_869
PDB_EXTRACT data extraction version: 3.11
Blu-Ice data collection
HKL-2000 data scaling
PHASER phasing