X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 289.0
Details Tris.HCl, sodium formate, glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289.0K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 206.2 α = 90
b = 206.2 β = 90
c = 295.41 γ = 120
Symmetry
Space Group P 62 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 173
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD CUSTOM-MADE -- 2002-07-22
Diffraction Radiation
Monochromator Protocol
Si(111) double-crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 1.0332 APS 19-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
2.75 100 98.8 -- 0.096 -- -- 95337 95337 -3.0 -3.0 --
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)
2.75 2.85 91.9 -- 0.461 -- -- --

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
MAD 2.8 8.0 -- 1.0 -- 82072 4386 99.41 -- 0.19587 0.19254 0.25884 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 2.8 2.864 5380 287 5380 0.319 0.368 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 48.355
Anisotropic B[1][1] 1.03
Anisotropic B[1][2] 0.51
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.03
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.54
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 2.89
r_bond_refined_d 0.013
r_angle_refined_deg 1.428
r_dihedral_angle_1_deg 6.153
r_chiral_restr 0.097
r_gen_planes_refined 0.004
r_nbd_refined 0.24
r_xyhbond_nbd_refined 0.181
r_symmetry_vdw_refined 0.219
r_symmetry_hbond_refined 0.272
r_mcbond_it 0.667
r_mcangle_it 1.291
r_scbond_it 1.621
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 13279
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 930

Software

Computing
Computing Package Purpose
HKL-2000 Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
SHARP Structure Solution
REFMAC 5.1.25 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.1.25 refinement