X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 293.0
Details 100mM Tris.Cl, 2.0M ammonium sulphate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 126.94 α = 90
b = 126.94 β = 90
c = 90.46 γ = 120
Symmetry
Space Group H 3

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
2 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD CUSTOM-MADE -- 2003-02-26
CCD CUSTOM-MADE -- 2003-02-28
Diffraction Radiation
Monochromator Protocol
double crystal SINGLE WAVELENGTH
double crystal MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-BM 0.97948 APS 19-BM
SYNCHROTRON APS BEAMLINE 19-ID 1.28348, 1.28402, 1.2574 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
1.9 50 99.9 0.063 -- -- 5.6 -- 42802 -- -- --
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)
1.9 1.97 100.0 0.599 -- -- 5.5 4251

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 1.9 10.0 -- 0.0 -- 42499 2146 99.95 0.196 -- 0.194 0.247 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 1.9 1.948 3007 127 2880 0.233 0.326 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 29.733
Anisotropic B[1][1] 0.17
Anisotropic B[1][2] 0.09
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.17
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.26
RMS Deviations
Key Refinement Restraint Deviation
r_bond_refined_d 0.01
r_nbtor_refined 0.305
r_sphericity_bonded 2.219
r_angle_refined_deg 1.232
r_sphericity_free 3.967
r_dihedral_angle_3_deg 15.372
r_symmetry_vdw_refined 0.197
r_scbond_it 1.9
r_mcangle_it 1.384
r_metal_ion_refined 0.23
r_chiral_restr 0.086
r_xyhbond_nbd_refined 0.157
r_symmetry_hbond_refined 0.162
r_nbd_refined 0.206
r_rigid_bond_restr 1.244
r_dihedral_angle_2_deg 34.689
r_dihedral_angle_4_deg 17.937
r_dihedral_angle_1_deg 5.733
r_mcbond_it 0.887
r_gen_planes_refined 0.004
r_scangle_it 2.868
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3822
Nucleic Acid Atoms 0
Heterogen Atoms 20
Solvent Atoms 358

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
SOLVE phasing version: 2.05
RESOLVE phasing version: 2.05
REFMAC refinement
PDB_EXTRACT data extraction version: 1.701