X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.4
Temperature 298.0
Details 17% PEG3350, 100mM Bis-Tris pH6.4, 200mM NH4NO3, 10mM Spermine HCl

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 106.48 α = 90
b = 106.48 β = 90
c = 303.73 γ = 90
Symmetry
Space Group P 43 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 93
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2015-02-20
Diffraction Radiation
Monochromator Protocol
Rosenbaum-Rock high-resolution double-crystal monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 0.9795 APS 19-ID

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
2.28 50 98.6 0.073 -- 24.316 7.0 -- 79060 -- -- 28.29
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)
2.28 2.32 99.8 0.89 -- -- 5.9 3929

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 2.285 45.718 -- 1.34 -- 116133 2991 76.83 -- 0.1791 0.1781 0.2185 --
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 2.2849 2.3224 -- 75 2833 0.2581 0.2734 -- 40.0
X Ray Diffraction 2.3224 2.3624 -- 86 3231 0.2541 0.2598 -- 46.0
X Ray Diffraction 2.3624 2.4054 -- 93 3464 0.2473 0.3076 -- 50.0
X Ray Diffraction 2.4054 2.4516 -- 95 3575 0.2445 0.2675 -- 51.0
X Ray Diffraction 2.4516 2.5017 -- 97 3716 0.2297 0.2801 -- 53.0
X Ray Diffraction 2.5017 2.5561 -- 99 3803 0.233 0.2614 -- 54.0
X Ray Diffraction 2.5561 2.6155 -- 109 4106 0.2139 0.2474 -- 59.0
X Ray Diffraction 2.6155 2.6809 -- 127 4680 0.222 0.2112 -- 67.0
X Ray Diffraction 2.6809 2.7534 -- 138 5249 0.2228 0.2462 -- 75.0
X Ray Diffraction 2.7534 2.8344 -- 155 5805 0.2277 0.2802 -- 83.0
X Ray Diffraction 2.8344 2.9259 -- 165 6273 0.2214 0.2913 -- 90.0
X Ray Diffraction 2.9259 3.0304 -- 175 6515 0.2138 0.2565 -- 93.0
X Ray Diffraction 3.0304 3.1517 -- 173 6656 0.2103 0.2658 -- 95.0
X Ray Diffraction 3.1517 3.2951 -- 180 6753 0.2027 0.2191 -- 96.0
X Ray Diffraction 3.2951 3.4688 -- 182 6723 0.1924 0.2186 -- 96.0
X Ray Diffraction 3.4688 3.686 -- 178 6721 0.1734 0.2444 -- 96.0
X Ray Diffraction 3.686 3.9705 -- 178 6704 0.1563 0.2129 -- 96.0
X Ray Diffraction 3.9705 4.3698 -- 172 6635 0.1397 0.1624 -- 95.0
X Ray Diffraction 4.3698 5.0014 -- 169 6648 0.118 0.186 -- 95.0
X Ray Diffraction 5.0014 6.2986 -- 174 6587 0.1518 0.1573 -- 94.0
X Ray Diffraction 6.2986 45.7273 -- 171 6465 0.1418 0.1852 -- 92.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 42.3238
RMS Deviations
Key Refinement Restraint Deviation
f_chiral_restr 0.026
f_dihedral_angle_d 12.556
f_bond_d 0.003
f_plane_restr 0.002
f_angle_d 0.617
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 10817
Nucleic Acid Atoms 0
Heterogen Atoms 60
Solvent Atoms 271

Software

Software
Software Name Purpose
PHENIX refinement
SCALEPACK data scaling
PDB_EXTRACT data extraction version: 3.15
Coot model building
HKL-3000 data collection