X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Hanging Drop Vapor Diffusion
pH 5
Temperature 295.0
Details PEG4000, NaCl, sodium acetate, Tris-HCl, pH 5.0, hanging drop vapor diffusion, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 84.49 α = 90
b = 84.49 β = 90
c = 60.87 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
-- -- -- 2008-10-08
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 24-ID-C 0.97949 APS 24-ID-C

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
1.8 50 99.9 0.043 -- -- 14.2 -- 20904 -- -- --
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)
1.8 1.83 100.0 0.443 -- -- 14.5 1012

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 1.8 49.39 -- 0.0 -- 20522 967 97.9 -- 0.231 0.23 0.248 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 1.8 1.847 -- 68 1328 0.239 0.316 -- 92.21
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 35.421
Anisotropic B[1][1] -0.5
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.5
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.0
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_1_deg 5.683
r_angle_refined_deg 1.367
r_scbond_it 2.028
r_gen_planes_refined 0.005
r_scangle_it 3.403
r_bond_refined_d 0.012
r_dihedral_angle_4_deg 19.815
r_dihedral_angle_2_deg 29.656
r_mcangle_it 1.186
r_dihedral_angle_3_deg 17.672
r_chiral_restr 0.096
r_mcbond_it 0.634
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1704
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 53

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
PHASER phasing
REFMAC refinement version: 5.4.0066
PDB_EXTRACT data extraction version: 3.006