X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.6
Temperature 293.0
Details 30% PEG MME 2000, 200mM Ammonium acetate, 100mM Sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 86.49 α = 90
b = 109.29 β = 90
c = 128.56 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 110
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD Beryllium lens 2009-10-23
Diffraction Radiation
Monochromator Protocol
C(111) diamond laue SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 21-ID-G 0.97857 APS 21-ID-G

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
1.6 50 99.0 0.081 -- -- 7.1 309132 306041 -- -- --
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)
1.6 1.66 97.6 0.626 -- 2.6 5.7 30186

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
SAD 1.6 29.04 2.6 0.0 160642 157911 7930 98.3 0.165 0.165 0.163 0.199 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 1.6 1.64 11104 555 9884 0.269 0.304 -- 89.08
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 8.44
Anisotropic B[1][1] -0.24
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.17
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.08
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_1_deg 5.66
r_dihedral_angle_3_deg 12.843
r_scbond_it 3.979
r_scangle_it 5.918
r_dihedral_angle_4_deg 18.132
r_bond_refined_d 0.013
r_dihedral_angle_2_deg 35.541
r_mcbond_it 1.409
r_angle_refined_deg 1.356
r_chiral_restr 0.099
r_gen_planes_refined 0.007
r_mcangle_it 2.328
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 10163
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 1295

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
REFMAC refinement
PDB_EXTRACT data extraction version: 3.005
BLU-MAX data collection
HKL-2000 data reduction
HKL-2000 data scaling
CRANK phasing