X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 293.0
Details 70% (v/v) MPD in 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 81.13 α = 90
b = 81.13 β = 90
c = 223.89 γ = 120
Symmetry
Space Group P 32 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD mirror 2006-03-08
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 22-ID 1.0 APS 22-ID

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
2.85 30 89.9 0.064 -- -- 4.6 18510 n/a 0.0 0.0 97.18
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)
2.85 2.95 75.2 0.304 -- 1.86 2.1 1509

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
FOURIER SYNTHESIS 2.85 29.11 -- 1.46 20724 18666 857 90.07 -- 0.2244 0.2213 0.2887 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 2.85 3.0287 2570 113 2570 0.3119 0.3671 -- 79.0
X Ray Diffraction 3.0287 3.2622 3104 153 3104 0.2621 0.318 -- 95.0
X Ray Diffraction 3.2622 3.59 2868 136 2868 0.2836 0.3587 -- 89.0
X Ray Diffraction 3.59 4.1082 2861 140 2861 0.2564 0.3668 -- 87.0
X Ray Diffraction 4.1082 5.1712 3226 158 3226 0.1779 0.2548 -- 97.0
X Ray Diffraction 5.1712 29.1118 3180 157 3180 0.207 0.2531 -- 92.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 116.776
Anisotropic B[1][1] 5.8512
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 5.8512
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -11.7024
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 14.699
f_plane_restr 0.003
f_chiral_restr 0.058
f_angle_d 0.698
f_bond_d 0.003
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3659
Nucleic Acid Atoms 1160
Heterogen Atoms 48
Solvent Atoms 22

Software

Computing
Computing Package Purpose
SERGUI Data Collection
HKL-2000 Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
CNS Structure Solution
PHENIX (phenix.refine: 1.7.3_928) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
SCALEPACK data reduction