X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.5
Temperature 289.0
Details 100mM sodium acetate, 2.9-3.3M sodium chloride, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 107.79 α = 90
b = 122.6 β = 90
c = 405.08 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2012-03-21
Diffraction Radiation
Monochromator Protocol
double crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRF BEAMLINE BL17U 0.97930 SSRF BL17U

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
2.89 50 95.4 0.175 -- -- 5.7 114675 114675 -- -- --
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)
2.9 3.0 95.4 0.805 -- -- 5.9 11309

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 2.893 48.884 -- 0.0 -- 109164 1949 90.52 -- 0.2395 0.2391 0.2618 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 2.8934 2.9658 -- 103 6243 0.3707 0.3582 -- 75.0
X Ray Diffraction 2.9658 3.046 -- 144 7004 0.3577 0.3495 -- 84.0
X Ray Diffraction 3.046 3.1356 -- 127 7328 0.3435 0.3757 -- 87.0
X Ray Diffraction 3.1356 3.2368 -- 138 7289 0.3224 0.3672 -- 88.0
X Ray Diffraction 3.2368 3.3524 -- 130 7534 0.2909 0.3235 -- 90.0
X Ray Diffraction 3.3524 3.4866 -- 131 7531 0.2771 0.2879 -- 90.0
X Ray Diffraction 3.4866 3.6453 -- 145 7697 0.25 0.3104 -- 92.0
X Ray Diffraction 3.6453 3.8374 -- 135 7838 0.2379 0.2688 -- 93.0
X Ray Diffraction 3.8374 4.0777 -- 152 7830 0.2174 0.2474 -- 93.0
X Ray Diffraction 4.0777 4.3923 -- 145 7954 0.2029 0.1885 -- 94.0
X Ray Diffraction 4.3923 4.834 -- 147 8014 0.1881 0.2003 -- 95.0
X Ray Diffraction 4.834 5.5327 -- 146 8075 0.2026 0.2308 -- 95.0
X Ray Diffraction 5.5327 6.9674 -- 145 8162 0.212 0.2534 -- 95.0
X Ray Diffraction 6.9674 48.8908 -- 161 8716 0.2295 0.2475 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 72.3225
Anisotropic B[1][1] 21.3315
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.3531
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -24.2773
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 9.663
f_plane_restr 0.002
f_chiral_restr 0.035
f_angle_d 0.559
f_bond_d 0.002
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 22127
Nucleic Acid Atoms 0
Heterogen Atoms 253
Solvent Atoms 19

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
PHENIX (phenix.refine: 1.7_650) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
SCALEPACK data reduction