X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 291.0
Details 1.0 M Sodium Malonate 0.05% jeffamine pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 106.68 α = 90
b = 106.68 β = 90
c = 146.16 γ = 90
Symmetry
Space Group P 43 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 325 mm CCD -- 2009-06-24
Diffraction Radiation
Monochromator Protocol
Double Crystal Monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL9-2 0.97946 SSRL BL9-2

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
2.94 50 95.8 -- -- -- -- -- 17789 -- -- --
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)
2.95 3.06 68.2 -- -- -- -- --

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 2.942 43.084 -- 1.0 -- 15979 775 86.09 -- 0.2186 0.2163 0.2623 --
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 2.9423 3.1265 -- 72 1637 0.3679 0.5431 -- 56.0
X Ray Diffraction 3.1265 3.3679 -- 139 2347 0.2952 0.2914 -- 82.0
X Ray Diffraction 3.3679 3.7066 -- 131 2563 0.2674 0.3297 -- 89.0
X Ray Diffraction 3.7066 4.2426 -- 120 2714 0.2028 0.241 -- 92.0
X Ray Diffraction 4.2426 5.3436 -- 127 2908 0.1656 0.1874 -- 98.0
X Ray Diffraction 5.3436 43.0884 -- 186 3035 0.207 0.2615 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 0.1145
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.1145
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.2291
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_dihedral_angle_d 22.694
f_angle_d 1.391
f_chiral_restr 0.079
f_bond_d 0.017
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2200
Nucleic Acid Atoms 468
Heterogen Atoms 44
Solvent Atoms 15

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
REFMAC refinement
PDB_EXTRACT data extraction version: 3.10
MAR345dtb data collection
REFMAC phasing
PHENIX refinement version: 1.6.4_486