X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6
Temperature 277.0
Details Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution:0.1M NaHPO4, 0.1M MES, PEG 20K 12%, VAPOR DIFFUSION, SITTING DROP, temperature 277KK

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 73.44 α = 90
b = 73.44 β = 90
c = 105.08 γ = 90
Symmetry
Space Group P 43 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 325 mm CCD Rh coated flat mirror 2011-05-12
Diffraction Radiation
Monochromator Protocol
Si 111 CHANNEL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL9-2 0.97918 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
1.6 50 100.0 0.05 -- -- 9.6 -- 72527 -- -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)
1.6 1.66 100.0 0.539 -- 4.1 8.9 --

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 1.6 29.039 -- 1.35 -- 38618 1932 99.92 -- 0.1808 0.1802 0.1928 --
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 1.5995 1.6395 -- 140 2557 0.2442 0.2402 -- 100.0
X Ray Diffraction 1.6395 1.6838 -- 135 2570 0.2191 0.2441 -- 100.0
X Ray Diffraction 1.6838 1.7333 -- 145 2572 0.1963 0.2095 -- 100.0
X Ray Diffraction 1.7333 1.7893 -- 131 2590 0.1843 0.2495 -- 100.0
X Ray Diffraction 1.7893 1.8532 -- 118 2585 0.1777 0.2102 -- 100.0
X Ray Diffraction 1.8532 1.9274 -- 157 2575 0.1646 0.1882 -- 100.0
X Ray Diffraction 1.9274 2.0151 -- 155 2568 0.1693 0.1937 -- 100.0
X Ray Diffraction 2.0151 2.1213 -- 139 2601 0.1654 0.1684 -- 100.0
X Ray Diffraction 2.1213 2.2542 -- 120 2630 0.1695 0.1797 -- 100.0
X Ray Diffraction 2.2542 2.4281 -- 138 2618 0.1727 0.2186 -- 100.0
X Ray Diffraction 2.4281 2.6723 -- 134 2648 0.1857 0.1914 -- 100.0
X Ray Diffraction 2.6723 3.0587 -- 133 2665 0.1817 0.2118 -- 100.0
X Ray Diffraction 3.0587 3.8522 -- 149 2678 0.1656 0.1704 -- 100.0
X Ray Diffraction 3.8522 29.0434 -- 138 2829 0.1918 0.1841 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] -0.708
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.708
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.4161
RMS Deviations
Key Refinement Restraint Deviation
f_chiral_restr 0.082
f_angle_d 1.214
f_bond_d 0.008
f_dihedral_angle_d 11.839
f_plane_restr 0.005
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1585
Nucleic Acid Atoms 0
Heterogen Atoms 19
Solvent Atoms 248

Software

Software
Software Name Purpose
PHENIX refinement version: 1.7.2_869
PDB_EXTRACT data extraction version: 3.100
ADSC data collection version: Quantum
DENZO data reduction
SCALEPACK data scaling
BALBES phasing