X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7
Temperature 295.15
Details 0.1 M sodium acetate pH 4.5, 30% w/V polyethylene glycol (PEG) 8000, and 0.2 M lithium sulfate

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 65.01 α = 90
b = 61.76 β = 91.53
c = 110.75 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS3 6M -- 2016-02-10
Diffraction Radiation
Monochromator Protocol
Liquid nitrogen-cooled double crystal monochromator, non fixed exit slit SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL9-2 0.976 SSRL BL9-2

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
2.95 40 91.8 0.129 -- -- 3.1 -- 17070 -- -- --
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)
2.95 3.06 67.5 0.283 -- -- 2.4 1237

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 2.95 40.0 -- 0.0 -- 16177 881 91.01 -- 0.2376 0.2353 0.2791 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 2.951 3.028 -- 50 747 0.283 0.33 0.0 60.15
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 71.576
Anisotropic B[1][1] -0.07
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.01
Anisotropic B[2][2] 0.0
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.07
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_2_deg 31.699
r_dihedral_angle_3_deg 15.361
r_bond_other_d 0.005
r_dihedral_angle_1_deg 6.172
r_chiral_restr 0.07
r_gen_planes_other 0.005
r_gen_planes_refined 0.005
r_dihedral_angle_4_deg 14.692
r_bond_refined_d 0.009
r_angle_refined_deg 1.485
r_angle_other_deg 1.27
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3923
Nucleic Acid Atoms 0
Heterogen Atoms 319
Solvent Atoms 91

Software

Software
Software Name Purpose
REFMAC refinement version: 5.8.0135
HKL-2000 data scaling
PDB_EXTRACT data extraction version: 3.22
HKL-2000 data reduction
PHASER phasing