X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 291.0
Details drop: 14 mg/mL protein, 0.8 M potassium phosphate, 5 mM Tris, 5 uM EDTA, 3.2% 1,2,3-heptanetriol, 2.0% dioxane, 140 mM sodium chloride, 0.045% LDAO, reservoir: 1.6 M potassium phosphate, cryoprotectant: 28% ethylene glycol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 138.87 α = 90
b = 138.87 β = 90
c = 185.49 γ = 120
Symmetry
Space Group P 31 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD -- 2010-03-11
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 21-ID-D -- APS 21-ID-D

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
2.97 120.26 99.2 0.094 -- -- -- -- 42919 0.0 -3.0 62.36
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)
2.97 3.05 99.9 0.762 -- 2.22 -- --

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 2.97 19.77 -- -- -- 42918 2146 100.0 -- 0.174 0.174 0.194 --
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 2.97 3.04 -- -- 3103 0.274 -- -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 53.84
Anisotropic B[1][1] 0.18
Anisotropic B[1][2] 0.09
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.18
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.27
RMS Deviations
Key Refinement Restraint Deviation
r_mcangle_it 2.28
r_scangle_it 5.553
r_bond_refined_d 0.035
r_angle_refined_deg 3.196
r_dihedral_angle_1_deg 8.747
r_dihedral_angle_4_deg 23.732
r_dihedral_angle_2_deg 35.22
r_scbond_it 3.589
r_dihedral_angle_3_deg 22.442
r_chiral_restr 0.189
r_gen_planes_refined 0.014
r_mcbond_it 1.212
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6465
Nucleic Acid Atoms 0
Heterogen Atoms 488
Solvent Atoms 52

Software

Software
Software Name Purpose
XSCALE data scaling
PHENIX refinement
PDB_EXTRACT data extraction version: 3.11
XDS data reduction
REFMAC phasing
REFMAC refinement version: 5.5.0109