X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 4.6
Temperature 293.0
Details 200 mM (NH4)2SO4, 30% (w/v) PEG2000MME, 100 mM sodium acetate 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 42.11 α = 90
b = 97.01 β = 90
c = 135.86 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 225 mm CCD -- 2010-05-07
Diffraction Radiation
Monochromator Protocol
DCCM SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SLS BEAMLINE X06DA 1.00000 SLS X06DA

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
1.67 30 99.8 -- -- -- -- 65578 65469 -3.0 -3.0 --
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)
1.67 1.71 99.4 -- -- -- -- --

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
PHASER 1.67 29.39 -- -- 62847 62847 2619 100.0 -- 0.18908 0.18765 0.22383 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 1.67 1.713 -- 189 4527 0.241 0.279 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 15.188
Anisotropic B[1][1] -0.2
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.5
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.3
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 3.617
r_scbond_it 2.581
r_mcangle_it 2.188
r_mcbond_other 0.658
r_bond_refined_d 0.011
r_bond_other_d 0.001
r_angle_refined_deg 1.418
r_angle_other_deg 0.872
r_dihedral_angle_1_deg 6.053
r_dihedral_angle_2_deg 31.525
r_dihedral_angle_3_deg 12.842
r_dihedral_angle_4_deg 10.511
r_chiral_restr 0.091
r_gen_planes_refined 0.006
r_gen_planes_other 0.001
r_mcbond_it 1.523
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4480
Nucleic Acid Atoms 0
Heterogen Atoms 83
Solvent Atoms 634

Software

Computing
Computing Package Purpose
SLS X06DA Data Collection
XDS Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
PHASER Structure Solution
REFMAC 5.5.0109 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.5.0109 refinement
PHASER model building
SLS version: X06DA data collection