X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop Nanodrop
pH 7
Temperature 277.0
Details 1.0M LiCl, 10.0% PEG-6000, 0.1M HEPES pH 7.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 140.03 α = 90
b = 96.64 β = 90
c = 115.78 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC -- 2005-01-22
Diffraction Radiation
Monochromator Protocol
Double Crystal Si(111) MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 8.2.1 0.97933, 1.00003,0.97951 ALS 8.2.1

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
1.73 28.61 99.9 -- 0.087 -- 3.8 -- 163581 -- -- 32.24
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)
1.73 1.82 100.0 -- 0.627 2.8 3.8 23624

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 1.73 28.61 -- -- -- 155289 8214 99.85 -- 0.15314 0.15164 0.18161 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 1.73 1.775 -- 646 11300 0.239 0.294 -- 99.92
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 24.051
Anisotropic B[1][1] 1.63
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.6
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.23
RMS Deviations
Key Refinement Restraint Deviation
r_symmetry_vdw_refined 0.134
r_symmetry_hbond_refined 0.22
r_nbd_other 0.181
r_bond_other_d 0.002
r_gen_planes_refined 0.008
r_dihedral_angle_2_deg 34.68
r_chiral_restr 0.102
r_nbtor_other 0.087
r_dihedral_angle_4_deg 16.847
r_symmetry_vdw_other 0.185
r_bond_refined_d 0.016
r_mcbond_other 0.601
r_angle_refined_deg 1.554
r_dihedral_angle_3_deg 11.412
r_nbd_refined 0.222
r_xyhbond_nbd_refined 0.187
r_angle_other_deg 0.879
r_metal_ion_refined 0.324
r_gen_planes_other 0.001
r_mcbond_it 1.963
r_nbtor_refined 0.193
r_scbond_it 5.03
r_dihedral_angle_1_deg 6.082
r_scangle_it 7.121
r_mcangle_it 3.083
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 8692
Nucleic Acid Atoms 0
Heterogen Atoms 161
Solvent Atoms 1098

Software

Software
Software Name Purpose
XDS data scaling
SCALA data scaling version: 5.0)
SHELXD phasing
SHARP phasing
REFMAC refinement version: 5.2.0005
XDS data reduction
CCP4 data scaling version: (SCALA)