X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.5
Temperature 293.0
Details 27% (w/v) PEG 3350, 0.3 M ammonium sulphate, 0.1 M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 76.94 α = 90
b = 90.31 β = 90
c = 154.56 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 25 Hz, 450 micron sensor thickness 2012-11-09
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 1.2395 PETRA III, EMBL c/o DESY P14 (MX2)

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
1.95 76.94 99.85 0.038 -- -- 12.88 79503 79385 -- -3.0 36.4
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)
1.95 2.06 98.59 0.49 -- 5.14 12.9 12489

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 1.95 68.97 -- -- 75286 75286 3977 99.65 0.17721 0.17721 0.17383 0.24356 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 1.947 1.998 -- 288 5305 0.192 0.342 -- 96.76
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 44.222
Anisotropic B[1][1] 0.33
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.35
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.67
RMS Deviations
Key Refinement Restraint Deviation
r_bond_refined_d 0.017
r_angle_refined_deg 1.846
r_dihedral_angle_1_deg 6.288
r_sphericity_bonded 26.704
r_dihedral_angle_3_deg 15.618
r_sphericity_free 23.818
r_dihedral_angle_4_deg 19.705
r_chiral_restr 0.13
r_gen_planes_refined 0.008
r_dihedral_angle_2_deg 36.005
r_rigid_bond_restr 7.444
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6141
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 195

Software

Software
Software Name Purpose
MxCuBE data collection
PHASER phasing
REFMAC refinement version: 5.7.0029
XDS data reduction
SCALA data scaling