X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6
Temperature 295.0
Details 0.1 M MES, pH 6.0, 4.0 M sodium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 162.51 α = 90
b = 162.51 β = 90
c = 60.99 γ = 90
Symmetry
Space Group P 42 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2012-04-10
Diffraction Radiation
Monochromator Protocol
Kozhu DCM Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON PAL/PLS BEAMLINE 5C 0.97948 PAL/PLS 5C

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
1.64 50 99.5 0.097 -- -- 12.0 -- 99377 -- -- --
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)
1.64 1.7 100.0 0.968 -- -- 12.1 9834

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 1.64 45.072 -- 1.34 -- 99311 2000 99.36 -- 0.2304 0.23 0.2464 --
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 1.64 1.6812 -- 139 6771 0.3236 0.3272 -- 98.0
X Ray Diffraction 1.6812 1.7266 -- 142 6883 0.2875 0.2865 -- 100.0
X Ray Diffraction 1.7266 1.7774 -- 142 6907 0.2725 0.2968 -- 100.0
X Ray Diffraction 1.7774 1.8348 -- 142 6926 0.2649 0.2867 -- 100.0
X Ray Diffraction 1.8348 1.9004 -- 142 6933 0.2514 0.2386 -- 100.0
X Ray Diffraction 1.9004 1.9765 -- 143 6919 0.2397 0.2547 -- 100.0
X Ray Diffraction 1.9765 2.0664 -- 142 6944 0.2426 0.2612 -- 100.0
X Ray Diffraction 2.0664 2.1754 -- 143 6974 0.2389 0.2575 -- 100.0
X Ray Diffraction 2.1754 2.3117 -- 143 6949 0.2394 0.2563 -- 100.0
X Ray Diffraction 2.3117 2.4901 -- 144 6978 0.2354 0.2531 -- 100.0
X Ray Diffraction 2.4901 2.7407 -- 144 7026 0.2394 0.2654 -- 100.0
X Ray Diffraction 2.7407 3.1372 -- 145 7041 0.2366 0.2258 -- 100.0
X Ray Diffraction 3.1372 3.9522 -- 144 7012 0.2016 0.2289 -- 98.0
X Ray Diffraction 3.9522 45.0889 -- 145 7048 0.2123 0.2335 -- 95.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 34.0994
Anisotropic B[1][1] -2.1546
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -2.1546
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 4.3091
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 15.727
f_plane_restr 0.004
f_chiral_restr 0.075
f_angle_d 1.139
f_bond_d 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4950
Nucleic Acid Atoms 0
Heterogen Atoms 88
Solvent Atoms 711

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
PHENIX Structure Solution
PHENIX (phenix.refine: 1.7.2_869) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
SCALEPACK data reduction