X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.6
Temperature 293.0
Details 30% PEG8000, 0.2M LiAc, 0.1M NaAc, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 42.43 α = 90
b = 129.94 β = 110.84
c = 44.39 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 180
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2011-07-22
Diffraction Radiation
Monochromator Protocol
GRAPHITE SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL44XU 1 SPRING-8 BL44XU

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
1.35 20 50.4 -- -- -- -- -- 99376 3.0 3.0 9.23
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)
1.35 1.4 100.0 -- -- -- -- --

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 1.35 19.825 -- 1.34 -- 97703 4879 99.62 -- 0.1347 0.133 0.1675 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 1.35 1.3982 -- 514 9231 0.1747 0.2197 -- 99.0
X Ray Diffraction 1.3982 1.4542 -- 474 9262 0.1476 0.1698 -- 100.0
X Ray Diffraction 1.4542 1.5204 -- 510 9259 0.1354 0.1575 -- 100.0
X Ray Diffraction 1.5204 1.6005 -- 486 9228 0.1263 0.1537 -- 100.0
X Ray Diffraction 1.6005 1.7007 -- 518 9300 0.124 0.1675 -- 100.0
X Ray Diffraction 1.7007 1.832 -- 509 9246 0.1255 0.1589 -- 100.0
X Ray Diffraction 1.832 2.0161 -- 476 9319 0.1305 0.1707 -- 100.0
X Ray Diffraction 2.0161 2.3075 -- 452 9291 0.13 0.1614 -- 100.0
X Ray Diffraction 2.3075 2.9058 -- 459 9353 0.1411 0.1834 -- 100.0
X Ray Diffraction 2.9058 19.8272 -- 481 9335 0.1276 0.1604 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 17.8113
Anisotropic B[1][1] 1.3339
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -1.927
Anisotropic B[2][2] -1.7726
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.4386
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 12.296
f_plane_restr 0.005
f_chiral_restr 0.069
f_angle_d 1.035
f_bond_d 0.006
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4226
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 1138

Software

Computing
Computing Package Purpose
ADSC Quantum Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
PHENIX Structure Solution
PHENIX (phenix.refine: 1.6.4_486) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.6.4_486) refinement
PHENIX model building
ADSC version: Quantum data collection