X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 291.0
Details 0.2 M zinc acetate, 0.1 M sodium cacodylate 6.5, 16% PEG8000, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 40.32 α = 90
b = 123.61 β = 90
c = 156.74 γ = 90
Symmetry
Space Group C 2 2 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 93
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2009-04-10
Diffraction Radiation
Monochromator Protocol
Si(111)side bounce monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 24-ID-E 0.9792 APS 24-ID-E

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
2.05 39.89 100.0 -- -- -- -- -- 47482 -- -3.0 --

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 2.05 39.89 -- 1.39 -- 47469 2385 99.94 -- 0.1901 0.188 0.231 --
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 2.05 2.1233 -- 254 4520 0.2567 0.3095 -- 100.0
X Ray Diffraction 2.1233 2.2083 -- 248 4471 0.2247 0.2746 -- 100.0
X Ray Diffraction 2.2083 2.3088 -- 246 4476 0.2132 0.2542 -- 100.0
X Ray Diffraction 2.3088 2.4305 -- 210 4527 0.1968 0.2625 -- 100.0
X Ray Diffraction 2.4305 2.5827 -- 221 4538 0.2021 0.2287 -- 100.0
X Ray Diffraction 2.5827 2.7821 -- 266 4493 0.1984 0.2802 -- 100.0
X Ray Diffraction 2.7821 3.062 -- 221 4528 0.1915 0.256 -- 100.0
X Ray Diffraction 3.062 3.5048 -- 237 4501 0.1743 0.2085 -- 100.0
X Ray Diffraction 3.5048 4.4148 -- 256 4512 0.1622 0.2055 -- 100.0
X Ray Diffraction 4.4148 39.9078 -- 226 4518 0.1831 0.2008 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 0.6758
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -4.739
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 4.0632
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.008
f_chiral_restr 0.067
f_dihedral_angle_d 11.954
f_angle_d 1.045
f_bond_d 0.006
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2993
Nucleic Acid Atoms 0
Heterogen Atoms 73
Solvent Atoms 155

Software

Computing
Computing Package Purpose
XDS Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
MOLREP Structure Solution
PHENIX (phenix.refine: 1.6.2_432) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
phenix refinement
MOLREP molecular replacement
Xscale data reduction