X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 298.0
Details 5% PEG8000, 8% ethylene glycol, 0.1 M HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 86.75 α = 90
b = 86.75 β = 90
c = 251.68 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 ADSC QUANTUM 315 -- 2010-07-25
Diffraction Radiation
Monochromator Protocol
double crystal Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 24-ID-C 0.97949 APS 24-ID-C

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
2 100 98.6 0.053 -- -- 4.0 -- 65257 -- -3.0 25.677
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)
1.998 2.07 99.4 0.218 -- -- 4.0 6436

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 1.998 59.595 -- 1.34 -- 65223 3311 98.63 -- 0.1715 0.1703 0.193 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 1.998 2.0266 -- 128 2490 0.1879 0.2209 -- 98.0
X Ray Diffraction 2.0266 2.0569 -- 130 2582 0.1731 0.211 -- 100.0
X Ray Diffraction 2.0569 2.089 -- 141 2541 0.1774 0.2044 -- 100.0
X Ray Diffraction 2.089 2.1233 -- 135 2604 0.1672 0.2088 -- 100.0
X Ray Diffraction 2.1233 2.1599 -- 139 2545 0.1635 0.1861 -- 100.0
X Ray Diffraction 2.1599 2.1992 -- 129 2582 0.1615 0.1782 -- 100.0
X Ray Diffraction 2.1992 2.2415 -- 136 2560 0.1594 0.1828 -- 99.0
X Ray Diffraction 2.2415 2.2872 -- 148 2579 0.1601 0.1723 -- 99.0
X Ray Diffraction 2.2872 2.3369 -- 129 2564 0.1544 0.1775 -- 99.0
X Ray Diffraction 2.3369 2.3913 -- 132 2552 0.1609 0.1869 -- 100.0
X Ray Diffraction 2.3913 2.4511 -- 128 2580 0.1624 0.2135 -- 99.0
X Ray Diffraction 2.4511 2.5174 -- 144 2576 0.1674 0.185 -- 100.0
X Ray Diffraction 2.5174 2.5915 -- 167 2555 0.1619 0.1739 -- 100.0
X Ray Diffraction 2.5915 2.6751 -- 133 2589 0.1628 0.1922 -- 100.0
X Ray Diffraction 2.6751 2.7707 -- 133 2613 0.159 0.1943 -- 100.0
X Ray Diffraction 2.7707 2.8817 -- 155 2586 0.1622 0.1852 -- 100.0
X Ray Diffraction 2.8817 3.0128 -- 115 2618 0.1671 0.1879 -- 99.0
X Ray Diffraction 3.0128 3.1716 -- 140 2597 0.168 0.2106 -- 100.0
X Ray Diffraction 3.1716 3.3703 -- 125 2637 0.1811 0.1989 -- 99.0
X Ray Diffraction 3.3703 3.6305 -- 145 2608 0.1782 0.2207 -- 98.0
X Ray Diffraction 3.6305 3.9958 -- 147 2562 0.1705 0.1958 -- 97.0
X Ray Diffraction 3.9958 4.5738 -- 137 2551 0.1534 0.1565 -- 95.0
X Ray Diffraction 4.5738 5.7618 -- 156 2524 0.1682 0.197 -- 93.0
X Ray Diffraction 5.7618 59.6215 -- 139 2717 0.2112 0.2055 -- 94.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 33.5746
Anisotropic B[1][1] 2.3459
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 2.3459
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -4.6918
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 13.036
f_plane_restr 0.005
f_chiral_restr 0.065
f_angle_d 1.058
f_bond_d 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4824
Nucleic Acid Atoms 0
Heterogen Atoms 1
Solvent Atoms 245

Software

Computing
Computing Package Purpose
ADSC Quantum Data Collection
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 1.7.3_928) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
phenix refinement
Phaser version: 2.1.4 molecular replacement
SCALEPACK data reduction