X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 293.0
Details PEG 8K, magnesium acetate, sodium cacodylate, lithium chloride, magnesium chloride, PAP, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 48.63 α = 90
b = 74.49 β = 90
c = 92.83 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
2 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARRESEARCH -- 2000-06-26
CCD ADSC QUANTUM 4 -- 2000-04-20
Diffraction Radiation
Monochromator Protocol
Si(III) monochromator SINGLE WAVELENGTH
Si(III) monochromator MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SRS BEAMLINE PX9.6 1.244 SRS PX9.6
SYNCHROTRON ESRF BEAMLINE BM14 0.97911, 0.97923, 0.91847 ESRF BM14

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
1.69 24.94 99.7 0.09 0.09 -- 5.3 38295 38295 0.0 0.0 13.0
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)
1.69 1.78 99.6 0.369 0.369 4.0 5.1 5441

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 1.69 24.94 0.0 0.0 38295 38295 1918 99.62 0.14866 0.14866 0.14696 0.18016 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 1.69 1.78 5541 -- -- 0.19 0.277 -- 99.6
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model isotropic
Mean Isotropic B 12.832
Anisotropic B[1][1] -0.29
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.47
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.18
RMS Deviations
Key Refinement Restraint Deviation
r_xyhbond_nbd_refined 0.235
r_bond_other_d 0.0
r_mcbond_it 1.496
r_nbd_other 0.195
r_gen_planes_refined 0.007
r_scbond_it 3.245
r_nbd_refined 0.236
r_symmetry_vdw_other 0.174
r_gen_planes_other 0.002
r_bond_refined_d 0.014
r_nbtor_other 0.199
r_dihedral_angle_1_deg 5.603
r_scangle_it 4.687
r_mcangle_it 2.354
r_symmetry_vdw_refined 0.068
r_dihedral_angle_3_deg 17.333
r_chiral_restr 0.111
r_angle_other_deg 1.94
r_angle_refined_deg 1.605
r_symmetry_hbond_refined 0.228
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2269
Nucleic Acid Atoms 0
Heterogen Atoms 35
Solvent Atoms 424

Software

Software
Software Name Purpose
SnB phasing version: v2.0
REFMAC refinement version: 5.0
DENZO data reduction
SCALEPACK data scaling