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_scangle_it 3.784
r_scbond_it 2.295
r_mcangle_it 1.452
r_mcbond_it 0.739
r_gen_planes_other 0.002
r_gen_planes_refined 0.006
r_chiral_restr 0.071
r_dihedral_angle_4_deg 16.48
r_dihedral_angle_3_deg 17.844
r_dihedral_angle_2_deg 34.081
r_dihedral_angle_1_deg 5.899
r_angle_other_deg 0.886
r_angle_refined_deg 1.319
r_bond_other_d 0.001
r_bond_refined_d 0.011
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

Computing
Computing Package Purpose
XDS Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
molrep Structure Solution
REFMAC 5.6.0117 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
REFMAC5 version: 5.5.0102 refinement
MOLREP molecular replacement
SCALA version: CCP4_3.3.9 data reduction