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 200 mM magnesium chloride, 30% (w/v) PEG4000, Tris hydrochloride ph 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 42.14 α = 90
b = 135.6 β = 95.73
c = 48.53 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD -- 2010-08-16
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
1.33 30 93.6 -- -- -- -- 123759 115868 -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)
1.33 1.36 63.7 -- -- -- -- --

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
MOLECULAR REPLACEMENT 1.33 29.93 -- -- 112379 112379 3476 100.0 -- 0.19088 0.19019 0.21313 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 1.33 1.364 -- 175 5649 0.233 0.272 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 10.977
Anisotropic B[1][1] -0.32
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.17
Anisotropic B[2][2] -0.47
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.82
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 1.952
r_scbond_it 1.554
r_mcangle_it 1.162
r_mcbond_other 0.463
r_bond_refined_d 0.011
r_bond_other_d 0.001
r_angle_refined_deg 1.41
r_angle_other_deg 0.94
r_dihedral_angle_1_deg 5.925
r_dihedral_angle_2_deg 33.202
r_dihedral_angle_3_deg 12.005
r_dihedral_angle_4_deg 11.894
r_chiral_restr 0.089
r_gen_planes_refined 0.007
r_gen_planes_other 0.005
r_mcbond_it 0.934
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4485
Nucleic Acid Atoms 0
Heterogen Atoms 39
Solvent Atoms 804

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