X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.8
Temperature 293.0
Details 19% PEG 6000, 600 mM NaCl, 3% Glycerol, 100 mM HEPES, 93 mM Tris-HCl, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 145.76 α = 90
b = 74.53 β = 131.87
c = 108.33 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD -- 2005-10-18
Diffraction Radiation
Monochromator Protocol
Fixed-exit LN2 cooled double crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SLS BEAMLINE X06SA 0.95008 SLS X06SA

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 50 96.9 0.073 -- -- 3.6 58793 56985 -- -3.0 37.05
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)
2.0 2.1 98.8 0.44 -- 4.32 3.7 7942

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
MIRAS 2.0 40.32 -- 0.0 56985 56985 2904 97.39 0.20524 0.20524 0.20395 0.22879 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 2.0 2.052 -- 218 4048 0.224 0.257 -- 99.12
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 31.78
Anisotropic B[1][1] -0.58
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.78
Anisotropic B[2][2] 1.22
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.67
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_2_deg 35.684
r_bond_refined_d 0.021
r_angle_refined_deg 1.832
r_scbond_it 3.273
r_nbtor_refined 0.319
r_symmetry_hbond_refined 0.235
r_mcangle_it 2.29
r_chiral_restr 0.137
r_mcbond_it 1.446
r_symmetry_vdw_refined 0.223
r_dihedral_angle_4_deg 22.079
r_nbd_refined 0.238
r_dihedral_angle_3_deg 16.77
r_xyhbond_nbd_refined 0.268
r_scangle_it 4.816
r_dihedral_angle_1_deg 7.053
r_gen_planes_refined 0.009
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5212
Nucleic Acid Atoms 0
Heterogen Atoms 83
Solvent Atoms 305

Software

Software
Software Name Purpose
XDS data scaling
SHARP phasing
REFMAC refinement version: 5.2.0019
XDS data reduction
XSCALE data scaling