X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8.3
Temperature 295.0
Details Protein: 7.3 mG/mL, 0.25 M Sodium chloride, 0.01 M Tris-HCL buffer pH 8.3; Screen: Classics II (H11), 0.1M Potassium thiocyanate, 30% (w/v) PEG 2000 MME., VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 80.22 α = 90
b = 80.22 β = 90
c = 174.25 γ = 120
Symmetry
Space Group P 63 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD Beryllium lenses 2013-11-26
Diffraction Radiation
Monochromator Protocol
Diamond SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F

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 30 99.8 0.056 0.056 -- 7.1 31574 31574 -- -3.0 27.2
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 0.512 0.512 3.9 7.2 1542

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 29.81 -- -- 29946 29946 1591 99.76 0.17403 0.17403 0.17272 0.1994 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 2130 125 2130 0.214 0.242 -- 99.91
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Thermal Factors Individually Isotropically Refined
Mean Isotropic B 35.616
Anisotropic B[1][1] 0.56
Anisotropic B[1][2] 0.28
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.56
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.82
RMS Deviations
Key Refinement Restraint Deviation
r_long_range_B_other 7.514
r_bond_refined_d 0.011
r_angle_refined_deg 1.558
r_chiral_restr 0.114
r_dihedral_angle_3_deg 11.49
r_dihedral_angle_4_deg 12.077
r_mcbond_other 1.87
r_gen_planes_other 0.001
r_mcangle_it 2.849
r_long_range_B_refined 7.609
r_dihedral_angle_1_deg 4.454
r_scbond_other 3.001
r_angle_other_deg 0.736
r_gen_planes_refined 0.007
r_scbond_it 3.007
r_scangle_other 4.628
r_bond_other_d 0.001
r_mcangle_other 2.85
r_dihedral_angle_2_deg 28.514
r_mcbond_it 1.88
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1865
Nucleic Acid Atoms 0
Heterogen Atoms 61
Solvent Atoms 206

Software

Software
Software Name Purpose
Blu-Ice data collection version: Max
PHASER phasing
REFMAC refinement version: 5.8.0046
HKL-3000 data reduction
HKL-3000 data scaling