X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 8.5
Temperature 298.0
Details 6% PEG 4000, 0.1M Tris, pH 8.5, 0.2M Lithium sulfate, vapor diffusion, hanging drop, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 130.35 α = 90
b = 199.63 β = 112.18
c = 150.15 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
XDSdataset 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
-- -- -- --
CCD RAYONIX MX-300 -- 2012-01-26
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON CLSI BEAMLINE 08ID-1 0.97949 CLSI 08ID-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
2.49 48.55 99.21 0.083 -- -- 4.24 -- 245749 -- -- --
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)
2.49 2.62 95.08 0.94 -- -- 4.0 --

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 2.49 48.07 -- -- -- 245706 12220 99.2 -- 0.207 0.204 0.263 --
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 2.49 2.56 -- 838 15486 0.328 0.378 -- 90.31
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 45.95
Anisotropic B[1][1] 0.336
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.579
Anisotropic B[2][2] 0.565
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.464
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_other 0.002
r_angle_refined_deg 1.319
r_bond_refined_d 0.011
r_bond_other_d 0.001
r_dihedral_angle_1_deg 5.899
r_mcbond_it 0.739
r_scangle_it 3.784
r_dihedral_angle_4_deg 16.48
r_scbond_it 2.295
r_dihedral_angle_3_deg 17.844
r_chiral_restr 0.071
r_angle_other_deg 0.886
r_gen_planes_refined 0.006
r_dihedral_angle_2_deg 34.081
r_mcangle_it 1.452
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 45085
Nucleic Acid Atoms 0
Heterogen Atoms 849
Solvent Atoms 260

Software

Software
Software Name Purpose
SCALA data scaling version: CCP4_3.3.9
MOLREP phasing
REFMAC refinement version: 5.5.0102
PDB_EXTRACT data extraction version: 3.11
XDS data reduction