X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.9
Temperature 291.0
Details 1.65M sodium phosphate monobasic monohydrate/potassium phosphate dibasic, 1% n-propyl formate., pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 334.05 α = 90
b = 334.05 β = 90
c = 177.57 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 200
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 210r -- 2012-12-10
Diffraction Radiation
Monochromator Protocol
double crystal monochromator MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0, 1.008, 1.06, 1.225 Photon Factory AR-NW12A

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
3.2 99 90.9 -- 0.114 -- 2.6 165225 150190 2.0 2.0 --
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)
3.2 3.31 92.2 -- 0.585 -- -- 15039

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
MAD 3.2 39.326 -- 0.0 150190 149279 7517 90.91 -- 0.228 0.226 0.2656 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 3.2 3.2363 -- 231 4775 0.3341 0.3802 -- 92.0
X Ray Diffraction 3.2363 3.2744 -- 271 4713 0.3172 0.3767 -- 93.0
X Ray Diffraction 3.2744 3.3143 -- 247 4757 0.307 0.3479 -- 93.0
X Ray Diffraction 3.3143 3.3562 -- 259 4776 0.3052 0.3283 -- 93.0
X Ray Diffraction 3.3562 3.4004 -- 244 4776 0.2967 0.3368 -- 93.0
X Ray Diffraction 3.4004 3.4469 -- 256 4777 0.2984 0.3154 -- 93.0
X Ray Diffraction 3.4469 3.4962 -- 265 4782 0.2909 0.3375 -- 93.0
X Ray Diffraction 3.4962 3.5483 -- 255 4788 0.2817 0.3176 -- 93.0
X Ray Diffraction 3.5483 3.6037 -- 256 4825 0.2636 0.3127 -- 93.0
X Ray Diffraction 3.6037 3.6628 -- 251 4777 0.2521 0.2968 -- 93.0
X Ray Diffraction 3.6628 3.7259 -- 244 4787 0.2475 0.3101 -- 93.0
X Ray Diffraction 3.7259 3.7936 -- 269 4797 0.2439 0.2738 -- 93.0
X Ray Diffraction 3.7936 3.8665 -- 251 4781 0.2394 0.2805 -- 93.0
X Ray Diffraction 3.8665 3.9453 -- 285 4735 0.2213 0.2738 -- 92.0
X Ray Diffraction 3.9453 4.031 -- 254 4749 0.2239 0.278 -- 92.0
X Ray Diffraction 4.031 4.1247 -- 242 4740 0.2192 0.2487 -- 92.0
X Ray Diffraction 4.1247 4.2277 -- 238 4751 0.2124 0.2423 -- 92.0
X Ray Diffraction 4.2277 4.3419 -- 241 4752 0.2008 0.2481 -- 91.0
X Ray Diffraction 4.3419 4.4695 -- 237 4749 0.2083 0.2651 -- 92.0
X Ray Diffraction 4.4695 4.6135 -- 278 4703 0.1991 0.245 -- 91.0
X Ray Diffraction 4.6135 4.7782 -- 228 4767 0.2004 0.2176 -- 91.0
X Ray Diffraction 4.7782 4.9691 -- 261 4731 0.2006 0.2403 -- 91.0
X Ray Diffraction 4.9691 5.1948 -- 261 4703 0.2078 0.2453 -- 90.0
X Ray Diffraction 5.1948 5.468 -- 241 4694 0.2157 0.2767 -- 90.0
X Ray Diffraction 5.468 5.8096 -- 247 4669 0.2327 0.2859 -- 89.0
X Ray Diffraction 5.8096 6.2565 -- 259 4642 0.2312 0.3058 -- 89.0
X Ray Diffraction 6.2565 6.8831 -- 241 4690 0.226 0.2743 -- 89.0
X Ray Diffraction 6.8831 7.8721 -- 243 4642 0.1997 0.2398 -- 88.0
X Ray Diffraction 7.8721 9.8919 -- 223 4581 0.1729 0.1843 -- 85.0
X Ray Diffraction 9.8919 39.3286 -- 239 4353 0.2031 0.2207 -- 78.0
RMS Deviations
Key Refinement Restraint Deviation
f_angle_d 1.108
f_bond_d 0.004
f_dihedral_angle_d 19.706
f_chiral_restr 0.072
f_plane_restr 0.004
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 56855
Nucleic Acid Atoms 0
Heterogen Atoms 226
Solvent Atoms 0

Software

Software
Software Name Purpose
HKL-2000 data collection
SOLVE phasing
PHENIX refinement version: (phenix.refine: 1.8_1069)
HKL-2000 data reduction
HKL-2000 data scaling