X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8.5
Temperature 277.0
Details 15.0000% Glycerol, 0.1700M NaOAc, 25.5000% PEG-4000, 0.1M TRIS pH 8.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 42.36 α = 90
b = 74 β = 90
c = 83.34 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 325 mm CCD Flat collimating mirror, toroid focusing mirror 2009-03-19
Diffraction Radiation
Monochromator Protocol
Double crystal monochromator MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL9-2 0.91837,0.97932 SSRL BL9-2

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
1.3 27.86 97.0 0.029 -- -- -- -- 64054 -- -3.0 12.925
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)
1.3 1.35 94.3 0.525 -- 1.7 -- --

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 1.3 27.864 -- 0.0 -- 63998 3240 98.15 -- 0.139 0.138 0.165 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 1.3 1.334 -- 234 4269 0.209 0.23 -- 94.92
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 18.041
Anisotropic B[1][1] 0.83
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.94
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.1
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_4_deg 12.154
r_mcangle_it 3.193
r_angle_refined_deg 1.745
r_dihedral_angle_2_deg 29.185
r_dihedral_angle_1_deg 5.242
r_scangle_it 6.267
r_mcbond_it 2.206
r_sphericity_free 8.725
r_gen_planes_other 0.002
r_rigid_bond_restr 1.826
r_dihedral_angle_3_deg 10.966
r_gen_planes_refined 0.007
r_angle_other_deg 1.41
r_scbond_it 4.387
r_bond_other_d 0.003
r_chiral_restr 0.105
r_mcbond_other 1.288
r_bond_refined_d 0.018
r_sphericity_bonded 4.735
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2196
Nucleic Acid Atoms 0
Heterogen Atoms 15
Solvent Atoms 312

Software

Software
Software Name Purpose
REFMAC refinement version: 5.5.0053
PHENIX refinement
SHELX phasing
MolProbity model building version: 3beta29
XSCALE data scaling
PDB_EXTRACT data extraction version: 3.006
XDS data reduction
SHELXD phasing
autoSHARP phasing