X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.6
Temperature 293.0
Details 65 mM KPi/22% PEG 8000, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 66.33 α = 90
b = 76.17 β = 90
c = 81.46 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 MARMOSAIC 300 mm CCD -- 2011-06-30
Diffraction Radiation
Monochromator Protocol
Sagitally Focused Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 22-BM 1.0 APS 22-BM

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
1.56 50 97.6 0.055 -- -- 5.0 -- 57746 2.0 2.0 --
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)
1.56 1.66 91.8 0.214 -- -- 3.2 --

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 1.56 22.767 -- 0.1 25272 57746 1993 97.15 -- 0.1414 0.1402 0.1775 --
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 1.5596 1.5986 -- 129 3720 0.152 0.2061 -- 92.0
X Ray Diffraction 1.5986 1.6418 -- 139 3831 0.1391 0.1916 -- 95.0
X Ray Diffraction 1.6418 1.6901 -- 134 3836 0.1229 0.1927 -- 95.0
X Ray Diffraction 1.6901 1.7446 -- 141 3889 0.1182 0.1693 -- 96.0
X Ray Diffraction 1.7446 1.807 -- 135 3894 0.116 0.1735 -- 96.0
X Ray Diffraction 1.807 1.8793 -- 142 3921 0.1191 0.1761 -- 97.0
X Ray Diffraction 1.8793 1.9648 -- 141 3956 0.1229 0.1671 -- 97.0
X Ray Diffraction 1.9648 2.0683 -- 143 4003 0.1311 0.1672 -- 98.0
X Ray Diffraction 2.0683 2.1978 -- 132 4047 0.1352 0.1696 -- 99.0
X Ray Diffraction 2.1978 2.3673 -- 154 4035 0.1359 0.1673 -- 99.0
X Ray Diffraction 2.3673 2.6052 -- 148 4051 0.1443 0.1919 -- 99.0
X Ray Diffraction 2.6052 2.9815 -- 150 4094 0.1571 0.1753 -- 99.0
X Ray Diffraction 2.9815 3.7536 -- 150 4162 0.1474 0.1639 -- 100.0
X Ray Diffraction 3.7536 22.7698 -- 155 4314 0.1512 0.1931 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 4.9417
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -2.9755
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.9662
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.006
f_chiral_restr 0.083
f_dihedral_angle_d 14.529
f_angle_d 1.656
f_bond_d 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3522
Nucleic Acid Atoms 0
Heterogen Atoms 77
Solvent Atoms 564

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
CNS Structure Solution
PHENIX (phenix.refine: 1.7.1_743) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
CNS molecular replacement
SCALEPACK data reduction
DENZO data collection