X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8.5
Temperature 291.0
Details 25% PEG3350, 0.2M magnesium chloride, 0.1M TRIS, pH 8.5, vapor diffusion, sitting drop, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 60.36 α = 90
b = 60.36 β = 90
c = 89.9 γ = 120
Symmetry
Space Group P 61 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD -- -- 2012-07-29
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 0.97931 APS 19-ID

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 50 99.8 0.09 -- -- 19.4 -- 7008 -- -- --
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)
2.0 2.03 100.0 0.958 -- -- 19.9 333

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 2.0 34.1 -- 0.0 -- 6972 322 99.59 -- 0.2181 0.2163 0.2508 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 2.0 2.053 -- 22 456 0.256 0.354 -- 97.35
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 56.8114
Anisotropic B[1][1] -1.57
Anisotropic B[1][2] -0.78
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.57
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 2.35
RMS Deviations
Key Refinement Restraint Deviation
r_bond_other_d 0.002
r_bond_refined_d 0.014
r_chiral_restr 0.088
r_angle_refined_deg 1.306
r_dihedral_angle_2_deg 23.445
r_dihedral_angle_4_deg 10.395
r_gen_planes_other 0.001
r_gen_planes_refined 0.005
r_dihedral_angle_1_deg 5.779
r_dihedral_angle_3_deg 12.549
r_angle_other_deg 0.704
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 536
Nucleic Acid Atoms 0
Heterogen Atoms 12
Solvent Atoms 22

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
PHASER phasing
REFMAC refinement version: 5.7.0027
PDB_EXTRACT data extraction version: 3.11