X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8.5
Temperature 289.0
Details 0.1 M Tris/HCl, 0.2 M LiSO4, 36 % PEG 4000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 74.13 α = 90
b = 146.84 β = 90
c = 58.48 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 MARMOSAIC 225 mm CCD -- 2006-12-08
Diffraction Radiation
Monochromator Protocol
-- MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X12 0.97885,0.97823,0.97240 EMBL/DESY, Hamburg X12

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
2.1 147.44 99.8 0.047 -- -- 4.9 37982 37982 1.0 -3.0 26.5
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)
2.1 2.21 24.4 0.161 0.214 8.1 4.1 5440

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 2.1 66.23 -- 0.0 37982 37952 1897 99.68 0.22168 0.22168 0.219 0.263 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 2.1 2.155 2745 140 2605 0.218 0.292 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 19.17
Anisotropic B[1][1] 3.31
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -2.51
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.79
RMS Deviations
Key Refinement Restraint Deviation
r_chiral_restr 0.078
r_symmetry_vdw_refined 0.182
r_scangle_it 3.07
r_dihedral_angle_1_deg 4.888
r_mcangle_it 1.058
r_dihedral_angle_3_deg 14.556
r_nbd_refined 0.204
r_mcbond_it 0.812
r_metal_ion_refined 0.103
r_bond_refined_d 0.011
r_gen_planes_refined 0.004
r_nbtor_refined 0.293
r_xyhbond_nbd_refined 0.217
r_dihedral_angle_4_deg 24.171
r_symmetry_hbond_refined 0.153
r_dihedral_angle_2_deg 41.488
r_scbond_it 2.062
r_angle_refined_deg 1.215
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4726
Nucleic Acid Atoms 0
Heterogen Atoms 58
Solvent Atoms 192

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0019
PDB_EXTRACT data extraction version: 3.005
MOSFLM data reduction
SCALA data scaling
SHARP phasing