X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.6
Temperature 298.0
Details 1.25 M lithium sulfate, 0.5 M ammonium sulfate, 0.1 M sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 77.63 α = 90
b = 66.82 β = 94.48
c = 64.83 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2011-12-08
Diffraction Radiation
Monochromator Protocol
double crystal Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 12.3.1 1.12 ALS 12.3.1

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
1.51 38.88 96.3 -- 0.035 -- 5.3 49769 49769 -- -- --
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)
1.51 1.55 94.0 0.682 0.682 1.1 5.3 3595

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 1.51 38.879 -- 1.36 -- 49765 2519 96.0 -- 0.1844 0.1827 0.2163 --
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 1.51 1.539 -- 158 2502 0.3127 0.3605 -- 94.0
X Ray Diffraction 1.539 1.5705 -- 143 2562 0.2813 0.3146 -- 94.0
X Ray Diffraction 1.5705 1.6046 -- 150 2576 0.2488 0.2764 -- 95.0
X Ray Diffraction 1.6046 1.6419 -- 148 2543 0.2455 0.2693 -- 94.0
X Ray Diffraction 1.6419 1.683 -- 157 2541 0.2318 0.2431 -- 95.0
X Ray Diffraction 1.683 1.7285 -- 135 2603 0.239 0.3093 -- 95.0
X Ray Diffraction 1.7285 1.7794 -- 130 2604 0.2168 0.2394 -- 95.0
X Ray Diffraction 1.7794 1.8368 -- 134 2641 0.2086 0.2111 -- 96.0
X Ray Diffraction 1.8368 1.9024 -- 119 2657 0.1933 0.2533 -- 96.0
X Ray Diffraction 1.9024 1.9786 -- 158 2595 0.1804 0.2154 -- 96.0
X Ray Diffraction 1.9786 2.0687 -- 136 2640 0.1733 0.1967 -- 97.0
X Ray Diffraction 2.0687 2.1777 -- 110 2671 0.1647 0.2024 -- 97.0
X Ray Diffraction 2.1777 2.3141 -- 154 2650 0.165 0.2013 -- 97.0
X Ray Diffraction 2.3141 2.4928 -- 151 2673 0.1594 0.1878 -- 98.0
X Ray Diffraction 2.4928 2.7436 -- 136 2696 0.1609 0.1961 -- 98.0
X Ray Diffraction 2.7436 3.1404 -- 114 2726 0.1716 0.2257 -- 98.0
X Ray Diffraction 3.1404 3.956 -- 144 2731 0.1689 0.2141 -- 99.0
X Ray Diffraction 3.956 38.8923 -- 142 2635 0.1886 0.1988 -- 94.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 30.2014
Anisotropic B[1][1] -5.1467
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -3.8131
Anisotropic B[2][2] 5.8846
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.7379
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 12.892
f_plane_restr 0.006
f_chiral_restr 0.075
f_angle_d 1.289
f_bond_d 0.011
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1874
Nucleic Acid Atoms 0
Heterogen Atoms 23
Solvent Atoms 321

Software

Computing
Computing Package Purpose
SCALA Data Reduction (data scaling)
PHENIX (phenix.refine: 1.7.3_928) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
SCALA version: 3.3.20 data reduction