X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 7.5
Temperature 295.0
Details 0.1 M calcium acetate, 0.1M Tris, 25-40% PEG 4000

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 40.16 α = 90
b = 81.29 β = 90
c = 97.43 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 RAYONIX MX-225 -- 2011-02-23
Diffraction Radiation
Monochromator Protocol
DCM MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON CLSI BEAMLINE 08ID-1 0.9793 CLSI 08ID-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
1.3 41.79 97.8 0.037 -- -- 7.2 -- 77516 -- -3.0 --
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)
1.3 1.33 81.5 0.604 -- 1.89 -- --

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 1.3 41.786 -- 1.99 -- 77513 2000 97.8 -- 0.1587 0.1583 0.1709 --
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 1.2999 1.3325 -- 116 4408 0.2651 0.2722 -- 81.0
X Ray Diffraction 1.3325 1.3685 -- 132 4947 0.2408 0.247 -- 91.0
X Ray Diffraction 1.3685 1.4088 -- 139 5273 0.2144 0.2206 -- 97.0
X Ray Diffraction 1.4088 1.4542 -- 145 5434 0.1851 0.1909 -- 100.0
X Ray Diffraction 1.4542 1.5062 -- 144 5489 0.1757 0.1843 -- 100.0
X Ray Diffraction 1.5062 1.5665 -- 145 5472 0.1543 0.1723 -- 100.0
X Ray Diffraction 1.5665 1.6378 -- 145 5447 0.1438 0.1936 -- 100.0
X Ray Diffraction 1.6378 1.7242 -- 145 5501 0.1425 0.1714 -- 100.0
X Ray Diffraction 1.7242 1.8322 -- 146 5490 0.149 0.1805 -- 100.0
X Ray Diffraction 1.8322 1.9736 -- 146 5521 0.1457 0.172 -- 100.0
X Ray Diffraction 1.9736 2.1723 -- 147 5514 0.1394 0.1448 -- 100.0
X Ray Diffraction 2.1723 2.4866 -- 147 5569 0.1421 0.1736 -- 100.0
X Ray Diffraction 2.4866 3.1326 -- 148 5621 0.1606 0.1537 -- 100.0
X Ray Diffraction 3.1326 41.8077 -- 155 5827 0.1588 0.1641 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 20.39
RMS Deviations
Key Refinement Restraint Deviation
f_angle_d 1.082
f_plane_restr 0.005
f_dihedral_angle_d 12.382
f_bond_d 0.006
f_chiral_restr 0.056
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2405
Nucleic Acid Atoms 0
Heterogen Atoms 154
Solvent Atoms 591

Software

Software
Software Name Purpose
XSCALE data scaling
XDS data reduction
PHENIX phasing
PHENIX refinement version: 1.8.1_1168
PDB_EXTRACT data extraction version: 3.20