X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 6.5
Temperature 294.0
Details 100mM sodium cacodylate pH 6.5, 1.4M sodium acetate hydrate, Vapor diffusion, temperature 294K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 82.01 α = 90
b = 82.01 β = 90
c = 32.37 γ = 120
Symmetry
Space Group P 31 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MAR CCD 165 mm -- 2008-07-18
Diffraction Radiation
Monochromator Protocol
diamond SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 31-ID 0.97958 APS 31-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
2.4 19.7 99.9 0.1 0.1 -- 22.0 5084 5079 0.0 0.0 51.6
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)
2.4 2.53 99.8 0.574 0.574 5.8 22.3 737

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 2.4 15.0 0.0 0.0 5054 5050 224 99.92 -- 0.226 0.225 0.243 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 2.4 2.461 353 11 353 0.349 0.389 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 36.837
Anisotropic B[1][1] -1.07
Anisotropic B[1][2] -0.54
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.07
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.61
RMS Deviations
Key Refinement Restraint Deviation
r_mcbond_it 0.924
r_nbtor_refined 0.307
r_metal_ion_refined 0.325
r_chiral_restr 0.09
r_gen_planes_refined 0.005
r_nbd_refined 0.241
r_symmetry_vdw_refined 0.436
r_angle_refined_deg 1.527
r_scbond_it 2.016
r_symmetry_metal_ion_refined 0.32
r_symmetry_hbond_refined 0.088
r_mcangle_it 1.708
r_xyhbond_nbd_refined 0.137
r_scangle_it 3.122
r_bond_refined_d 0.014
r_dihedral_angle_2_deg 37.687
r_dihedral_angle_3_deg 17.773
r_dihedral_angle_1_deg 6.364
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 600
Nucleic Acid Atoms 0
Heterogen Atoms 1
Solvent Atoms 5

Software

Software
Software Name Purpose
SCALA data scaling version: 3.2.19
REFMAC refinement
PDB_EXTRACT data extraction version: 3.006
MAR345 data collection version: CCD
MOSFLM data reduction
SHELXCD phasing
SHELXE model building