X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5
Temperature 298.0
Details 0.1M Na Acetate, 0.8M Amm. Sulfate, 100mM Cadmium chloride, 10% n-Decyl-B-D-maltoside, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 73.58 α = 90
b = 73.58 β = 90
c = 92.3 γ = 90
Symmetry
Space Group P 41 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 113
Diffraction Detector
Detector Diffraction Type Details Collection Date
DIFFRACTOMETER RIGAKU AFC-5R -- 2001-09-15
Diffraction Radiation
Monochromator Protocol
Graphite SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON MPG/DESY, HAMBURG BEAMLINE BW6 1.5418 MPG/DESY, HAMBURG BW6

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 15 97.3 -- 0.066 -- 13.3 32368 31495 -- 2.0 --
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 93.8 -- 0.515 5.4 11.3 3339

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 1.6 8.0 -- 4.0 -- 31495 1633 97.3 0.295 0.2533 0.2522 0.27291 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 1.641 -- 109 2114 0.356 0.371 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 12.751
Anisotropic B[1][1] 0.14
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.14
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.28
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_1_deg 5.962
r_scangle_it 2.234
r_gen_planes_refined 0.004
r_symmetry_vdw_refined 0.334
r_xyhbond_nbd_other 0.234
r_mcbond_it 0.53
r_symmetry_hbond_refined 0.352
r_scbond_it 1.565
r_bond_refined_d 0.017
r_angle_refined_deg 1.29
r_chiral_restr 0.082
r_xyhbond_nbd_refined 0.208
r_nbd_refined 0.228
r_mcangle_it 0.904
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1647
Nucleic Acid Atoms 0
Heterogen Atoms 4
Solvent Atoms 104

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
AMoRE phasing
REFMAC refinement version: 5.1.24