X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 295.0
Details PEG 8000, Na cacodylate, Ca acetate, Glycerol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 72.08 α = 90
b = 72.08 β = 90
c = 245.56 γ = 120
Symmetry
Space Group P 65 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 110
2 110
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD CUSTOM-MADE Sagitally focusing double crystal monochromator and vertically focusing mirror 2002-06-07
CCD CUSTOM-MADE Sagitally focusing double crystal monochromator and vertically focusing mirror 2002-03-17
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Si(111) MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 0.9795, 0.9793, 0.9537 APS 19-ID
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
1.95 60 99.6 -- 0.072 -- -- 28687 28572 -- 0.0 --
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)
1.95 2.01 100.0 -- 0.468 5.0 -- 2457

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 1.95 62.02 -- 0.0 28572 26023 1389 95.85 0.18897 0.18897 0.18708 0.22493 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 1.95 2.001 -- 101 1745 0.202 0.269 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 18.524
Anisotropic B[1][1] 0.45
Anisotropic B[1][2] 0.23
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.45
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.68
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_other 0.003
r_symmetry_hbond_refined 0.207
r_angle_refined_deg 1.814
r_nbd_refined 0.244
r_scbond_it 2.941
r_nbtor_other 0.092
r_scangle_it 4.486
r_angle_other_deg 1.176
r_bond_refined_d 0.024
r_mcbond_it 1.129
r_bond_other_d 0.003
r_dihedral_angle_1_deg 5.646
r_xyhbond_nbd_refined 0.178
r_symmetry_vdw_refined 0.246
r_mcangle_it 1.875
r_nbd_other 0.268
r_chiral_restr 0.11
r_symmetry_vdw_other 0.284
r_dihedral_angle_3_deg 19.146
r_gen_planes_refined 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2807
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 205

Software

Software
Software Name Purpose
d*TREK data scaling
dtDisplay data collection
HKL-2000 data reduction
CNS refinement
REFMAC refinement version: 5.0
d*TREK data reduction
DTDISPLAY data reduction
HKL-2000 data scaling
CNS phasing