X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 298.0
Details drop: 13 mg/mL protein, 0.8 M potassium phosphate, 5 mM Tris, 5 uM EDTA, 4.0% 1,2,3-heptanetriol, 2.0% dioxane, 140 mM sodium chloride, 0.045% LDAO, reservoir: 1.6 M potassium phosphate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 139.72 α = 90
b = 139.72 β = 90
c = 183.98 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 -- 2012-03-23
Diffraction Radiation
Monochromator Protocol
diamond(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 21-ID-G -- APS 21-ID-G

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
2.93 121 99.6 0.125 -- -- -- -- 45001 0.0 -3.0 55.99
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)
2.93 3.01 100.0 0.793 -- 2.89 -- --

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 2.93 121.0 -- -- -- 44997 2250 99.6 -- 0.187 0.185 0.226 --
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 2.93 3.01 -- 163 3100 0.265 0.323 -- 99.97
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 48.49
Anisotropic B[1][1] -0.03
Anisotropic B[1][2] -0.01
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.03
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.04
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_refined 0.009
r_dihedral_angle_3_deg 21.08
r_scbond_it 2.306
r_bond_refined_d 0.021
r_scangle_it 3.655
r_dihedral_angle_1_deg 7.376
r_mcangle_it 1.558
r_angle_refined_deg 2.364
r_chiral_restr 0.138
r_dihedral_angle_2_deg 35.199
r_mcbond_it 0.806
r_dihedral_angle_4_deg 23.924
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6391
Nucleic Acid Atoms 0
Heterogen Atoms 507
Solvent Atoms 21

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